In the 3D Background Explanations Corner of the Mahou Sensei Negima! volumes, whenever Ken Akamatsu notes that something is off, like how the external shots of Eva's home doesn't match the internal shots, he'd mention with his tongue firmly in cheek that it's probably due to magic screwing up its physical dimensions or something similar.
Yotsuba invokes this trope in chapter 68 to try to squirm out of trouble when she breaks some dishes, to patch up holes in her story. Her father doesn't buy it for a second.
Played for laughs in the pornographic mangaSei Sou Tsui Dan Sha: So how was it possible that the main character's penis could be detached from his body, and reattached to anyone else? Magic. His mom was a witch this whole time. Yes, he knew about this, but didn't think to tell anyone until she mentioned it herself. And yes, all this is divulged in exactly one page and MariItsuki is not taking it well.
DC Comics used an in-character plot device in the Infinite Crisis miniseries to justify various RetCons and mistakes. "Superboy punch!" is now the standard response among fandom to questions about inconsistencies; this replaces the refrain of "Hypertime!", contributed by a previous miniseries, The Kingdom.
People acting Out of Character these days is blamed on Deathstroke's mind altering drugs, primarily because this was the canon (via Retcon) explanation for Cassandra Cain Batgirl's poorly executed Face-Heel Turn after Infinite Crisis.
"Deathstroke's drugs" are the DC equivalent of Marvels "Skrull imposter".
Due to the Secret Invasion revelation that Skrulls have been impersonating heroes, running around as extra copies of the heroes (particularly ones of Wolverine), brainwashed into thinking like the heroes, brainwashed into thinking that they are the heroes, are actually heroes who happen to also be Skrulls, and that now at least one of the Skrull impersonators has been replaced by another Skrull, the explanation that any character seen as being Out of Character or using their powers in ways they can't is really a Skrull has become pretty popular.
Thanos lookalikes are often used in the same manner. After Squirrel Girl (hilariously) defeats him and Uatu states that it is definitely the real Thanos, it's later revealed that Thanos can create lookalikes which can fool even Uatu. Or so he claims.
A writer of "Marvel Zombies" Handwaved everything in the series, by saying that it was another universe, and thus justified any inconsistencies it had with that of the Earth-616 universe. (e.g. Reed Richards being evil and Galactus having an actual, physical body that the zombies can eat)
"The code libraries from Elysium had all sorts of modules for letting people take their own environments with them and making the rules interact - they spent a lot of time trying to entertain themselves - so I picked one of the standard tools that had a really simple interface, where I just needed to answer a few yes-or-no questions to make it happen automatically -" "A wizard did it!" shouted a buxom woman in black leather armor with a silver hoop strapped to her thighs. There was widespread laughter, and not a few groans of agony.
In With Strings Attached, when the four are in the Hunter's world, John tells the others that he thinks the Poison Swamp was created artificially, with magic. Why? “I quit wonderin' about motivations on other planets. I just assume everyone's daft, and that pretty much covers it.”
Quite a bit of The Emiya Clan revolves around one of the rather annoying magicians that hang around the family doing something silly to mess things up (and occasionally fix them, but only occasionally). Lampshaded at one point.
Queen Of All Oni: Jade writes this off as the explanation for how Shendu's palace is in partially intact ruins, despite completely disintegrating the last time she was there.
Viper likewise uses this as the word-for-word explanation when Jackie wonders how Kuro's mask ended up buried inside a cliff face, halfway up it.
In Star Wars, especially the Expanded Universe, The Force, in addition to giving selected characters their "magical" abilities, seems to double as a convenient way to explain away plot holes or especially unbelievable plot devices.
It's been observed that when you replace references to "the Force" in Star Wars with "the Plot", the dialogue actually makes more sense.
The standard explanation for any continuity errors in the new Star Trek movie is, "A particularly troubled time-traveling Romulan did it." Even when those errors date from BEFORE the Romulan split the timeline. The Contrived Coincidences get a version where the timeline is trying to repair itself.
In a meta example from The Lord of the Rings films, during an interview director Peter Jackson praised the humility and amiability of Sir Ian McKellen. He recalled an example regarding the siege of Gondor, which is paraphrased:
McKellen: Why doesn't Gandalf just use his magic to defeat them all?
Jackson: The staff is out of batteries, and because of the war the alchemist's shop is closed and he can't get new ones.
The actual reason is an aversion, since there's a genuine plot-logic reason: if Gandalf uses his full power, Sauron will have an incentive to take a personal hand in the fight—and he's a stronger Maia than Gandalf, so he'll win. Having been forced to take a personal hand, Sauron would then defeat all Gandalf's allies (who would be screwed without him anyway), and, with his schedule freed up, might notice a couple of Hobbits stumbling around at the foot of Mount Doom.
More to the point, Gandalf's order of Istari were sent to Middle Earth with a mission to rally the free peoples to defeat Sauron, not to do it themselves. They were expressly forbidden to match Sauron's power with power.
In the Men In Black movies, pretty much anything unusual or seemingly impossible the MiBs do can be explained by the existence of alien technology. Of course the big things like time travel and rocket cars are obvious, but it pretty much covers everything right down to the small details. Asking how K can hang upside down in an elevator or how Zed can jump around a room while fighting an alien despite his advanced age, could be explained as Imported Alien Phlebotinum and MiB's Crazy Preparedness.
Older Than Steam: In Don Quixote, whether his beloved Dulcinea appears to be a garlic-chewing peasant, or our hero is transported from his inn chamber to fight a giant (who is actually a passel of wineskins hung above his bed), Don Quixote believes it is due to malevolent enchanters. This doesn't quite count as an example, as the text makes it clear that there is no magic occurring and Don Quixote is quite deluded when he believes such things. The book is trying to make fun of earlier books that used this trope.
In the Discworld novel Thief of Time, most of the inconsistencies and ambiguities in the Discworld timeline (as well as some of the Schizo Tech) are implied to be the result of the first Glass Clock shattering history, or side effects of the History Monks cleaning up afterwards. They describe how they moved "excess time" to where it wouldn't be noticed (such as deep in the ocean) and likewise moved time from such places when required. The fact that most characters fail to notice the inconsistencies (like, for example, Ankh-Morpork having a 16th century Shakespearean theater across the river from a 19th century opera house, and the same characters appearing in two books set nearly a century apart) is explained by the fact that most people only notice what they expect to notice.
Terry Pratchett has declared that all timelines are correct, but some went down different legs of the "Trousers of Time." He's also phrased it as, "There are no continuity errors in the Discworld novels. There are, however, alternate pasts."
John Dies at the End has an example of this, in a similar vein to Discworld, outside the books. Back before it was published, the author, David Wong had a couple of possible inconsistencies pointed out. His response? "There are no plot-holes: just more layers of mystery".
Xanthretconned its considerable continuity errors in Geis of the Gargoyle, where it's revealed that the expanding "Region of Madness" has caused odd fluctuations in people's magical talents. For example, at one time the Gorgon could only turn men into stone with her gaze; later her powers worked on women as well.
In addition to allowing the two to travel through time in Time Cat, Gareth's cat powers allow Jason to blend in to his temporal and cultural surroundings nearly seamlessly. It gives him Translator Microbes, adapts his clothes to current fashions and presumably keeps him from contracting common pathogens of the times and dying of salmonella or something before he gets back home.
In Power Ranger, Forever Red gives no exclamation while some rangers suddenly have their powers again. Once A Ranger attempts this trope by simply having The Sentinel Knight restoring their powers with little more than a handwave. One wonders why he didn't use those powers to temporarily restore the Overdrive rangers powers while they got the morphing grid back on.
Buffy the Vampire Slayer. Living in Sunnydale (which is on top of a Hellmouth) is a convenient explanation for many aspects of the show which would be ludicrous or impossible otherwise.
Principal Snyder's standard excuse was "gang on PCP."
"It could be witches! Some evil witches! Which is ridiculous 'cause witches, they were persecuted, wicca good, and love the earth, and women power, and I'll be over here..."
Doctor: "There was a goblin, or a trickster. Or a warrior. A nameless, terrible thing soaked in the blood of a billion galaxies. The most feared being in all the cosmos. And nothing could stop it, or hold it or... reason with it. One day it would just drop out of the sky and tear down your world."
Amy: "How did it end up in there?"
The Doctor: You know fairy tales — a good wizard tricked it."
River: "I hate good wizards in fairy tales. They always turn out to be him."
LOST: When you don't understand what's happening, just tell yourself "The island did it". Or more specifically, Jacob and the MIB did it, with magical Island-granted powers.
Inconsistencies in the Moffat era are usually explained away by blaming them on the Cracks in Time and the subsequent rebooting of the universe (aka Big Bang Two). On this very wiki, the phrase "timey-wimey" is used to explain just about everything.
In possibly an inversion, when it's asked why the Doctor doesn't do something, fans are often quick to suggest it was a fixed point in time.
How is that all five of the Final Five managed to survive the Cylon destruction of the Twelve Colonies in Battlestar Galactica? Along with an admiral whose family had history with the creator of the Cylons? And the Colonials and Cylons converge on the Algae Planet and in the Ionian Nebula despite the size of the universe? No doubt the higher power that doesn't like to be called "God" is responsible. Lampshaded in the Final Five and Algae Planet cases.
Partially explained in "The Plan". Cavil was working behind the scenes to make sure the Final Five survived so they could suffer even more.
Some Sci-Fi series, and Star Trek in particular, have their own variation: A Time Traveler Did It. This didn't get much use for the first several series, but by the later seasons of Voyager it could be a standard reason; now, ever since Enterprise rolled out its Temporal Cold War, the sky's the limit on this one.
If somehow a time traveler couldn't have done it, then just assume that Q did it.
Indeed, this seems to be the trope on which the plot of JJ Abrams' reboot hangs.
Warehouse 13 uses several variations on the theme. For instance, the electric Stun Guns Warehouse Agents carry were invented by Nikola Tesla (a very standard way of explaining late-era Steam Punk tech) and the Diesel Punk-looking iPhones they carry were invented by Philo Farnsworth (one of several people credited with inventing the television).
In DVD Commentaries for Merlin, actress Katie McGrath coined the term "talking dragon" to cover for any inconsistencies in the plot, pointing out that anything is possible when a talking dragon is part of the main cast.
Credence Clearwater Revival's "Looking Out My Back Door" provides the following explanation for the strange imagery of the song:
Tzeentch did it in normal Warhammer, too. He's been working carefully for ~40,000 years and it still doesn't make any damn sense. Making no damn sense is Tzeentch's hat. Everything Tzeentch does is part of some master plan of his. However, it's impossible to tell what this plan is actually for, because its elements seem nonsensical, self-contradictory and — as befitting a Chaos God — utterly chaotic. It's possible it doesn't actually have an end goal — planning is part of his nature, but no-one said his plans have to make sense or actually accomplish anything.
Actually he CAN'T have an end goal, because if he wins then he doesn't plot anymore and he can't exist without plotting. So really, continued plotting is his end goal.
Many bizarre, inexplicable, or just plain silly monsters from the early days of Dungeons & Dragons were said to be the product of wizards playing Evilutionary Biologist in their spare time. Even gnolls were initially reputed to be the result of A Wizard Did It. The classic example is the owlbear.
Most of the more bizarre content in Spelljammer is explained by A Wizard Did It. Sometimes literally. One sourcebook actually explains the sheer weirdness of the setting with "It's magic, and it knows it's magic."
Q: Can my opponent do something that doesn't make sense, such as casting both Holy Strength and Unholy Strength on his Air Elemental?
A: Yes, these effects are magical, after all.
Some rules interactions lead to very active wizards. Probably the two biggest examples are equipment (magical items like enchanted swords that can be used by creatures) and walls (treated like creatures by the rules, but generally meant to symbolize inanimate objects). Now picture a stone wall USING an enchanted sword...
Walls (at least the non-black, non-artifact ones) can potentially drop dead of fright in this game. At least one card's flavor text lampshades this.
White Wolf eventually took the position that everything written in the Warcraft RPGs were actually in-universe documents, and any errors was the result of bad information. Some portions of the books do look like they could've been in-universe (several books are almost entirely written by one guy); other parts, not so much.
In the new edition of Gamma World, one of the suggestions they give for how to reconcile the Plant and Android character origins boils down to A Wizard Did It when you strip out the setting jargon and Technobabble — it suggests that you hail from a remote worldline (Some exotic place the players will probably never see), where Psionic masters (Wizards) create golem-like servants out of plant matter. (Your character, which exists because A Wizard Did It)
The French have a phrase to express it : "Ta gueule, c'est magique" (Shut up, that's magical). It often pops up when a Game Master is asked questions about something in his campaign. It's often shortened to TGCM or TGM. In English it's SUIM (shut up—it's magic).
In Exalted, the answer to such questions is almost inevitably "An Exalt did it." If not an Exalt, then a Primordial. If not a Primordial, then a god. If not a god, it was probably belched up by the Wyld.
This trope is in full effect in Shakespeare's final play: The Tempest. The plot begins with Prospero; a wizard, conjuring a storm which bring most of the other characters to his (Prospero's) island. From there on, nearly every plot development stems from some further act of magic on the wizard's behalf. Some Lampshade Hanging also occurs, as the script repeatedly comments on magic being the solution to inconsistencies in the plot.
In Dragon Fable In the Gate Keeper Quest Artix uses this to hand wave the fact that you have Zorbak's ID Card so you can get into the Necropolis. To clarify the many problems that came up:
The ID's picture looks nothing like your character.
The ID is expired.
The ID says Zorbak was expelled.
In Nethack, the "Wizard" mode lets you spawn items/creatures at will, have unlimited wishes and reveal maps instantly. After all, you are a wizard...
And if something unexplainable happens during normal game, A mysterious Force did it. If you try to teleport on a no-teleport level, a mysterious force prevents you from teleporting. If you try to descend the stairway to your quest without permission, a mysterious froce prevents you from descending. If the Amulet of Yendor teleports you down, a mysterous force momentary surrounds you. If you are digging with a blessed pickaxe in the endgame a mysterious force forms a cave.
And if something nasty happens to you after the invocation (like having your invetory cursed or swarms of monsters appearing out of nowhere) a literal Wizard did it ... The Wizard of Yendor.
Seen often in the Resident Evil video game series, but replace "wizard" with "Albert Wesker."
Resident Evil: Umbrella Chronicles actually explains HOW he did some of the more wizardy things. And for those things the wizard did to HIM, well, Birkin did it.
Also appears in the Metroid games, specifically in the Prime subseries, in which the radioactive Phlebotinum Phazon is used by fans to explain away multiple inconsistencies and completely random evolutions.
In the other games, however, the Chozo did it. In Prime 1, it was both!
Other M attempts to subvert this by doing away with with the Chozo. Goes to show that Tropes Are Not Bad, as it ended up creating a whole lot of plot holes without an easy and accessible Handwave, leaving fans to latch on the next best thing and saying Adam did it despite the fact he dies, or the Deleter, or Mother Brain.
The developers for World of Warcraft have stated multiple times that they are more interested in making game play fun than specifically following established mythology. As a result, much of the story established in the RTS Warcraft games has been retconned in World of Warcraft to better fit certain gameplay mechanics. The popular explanation on message boards from both players and moderators is "a wizard did it".
A mutant of this has become a meme among the players of the MMORPG City of Heroes: "If it doesn't make sense, it's a Nemesis Plot." Nemesis himself is a supervillain who is infamous for making plots within plots within plots and is revealed to be a driving force, or at least the root cause, of many of the conflicts going on in the game.
Or, as the loading screens now lampshade this: "Everything is a Nemesis plot." Also on loading screens: "Not everything is a Nemesis plot."
The contacts Crimson and Indigo, who's missions deal with the black ops Malta Group, will often tell you that you need to go somewhere for a mission to save someone or something, but the reasons why this needs to be done are classified, so they can't tell you why. They can take three paragraphs to say this too.
The two common explanations for the many inconsistencies that reside in the Touhou Universe and backstory are either that Keine ate it, or that Yukari was messing around with the borders of space and time again.
The Elder Scrolls II: Daggerfall allowed the player to choose one of several endings with supposedly world-changing effects. This left the developers in a sticky place when it came time for the sequel, The Elder Scrolls III: Morrowind, so they invented a supernatural disaster, "The Warp in the West", in which all the endings to Daggerfall had happened at once.
Oddly enough, this led to endings which contradicted one another occurring simultaneously. Mannimarco, the first Lich, both succeeded and didn't succeed in making himself a god, meaning he has a divine incarnation and a mortal (but undead) avatar at the same time. The Dragon Break (as it was also called) also makes the ending where the player character is crushed to death in a meaningless happenstance true as well.
In the Shivering Isles expansion for The Elder Scrolls IV: Oblivion, one quest has the player dealing with a town full of duplicates. When asked how the duplicates came about, the quest-giving NPC only tells you A Wizard Did It.
In the later games in the Myst series, Yeesha becomes able to break the rules horribly - intra-age linking, books that follow you through the link, books that send different people to different copies of the same age. You name it, she can do it. And we're never really told how, except that she's the only one who can.
Given her father is Atrus and how he was able to write changes into Riven without resetting the Age, as well as the daughter of Catherine, who wrote Torus, a doughnut-shaped Age, being able to bend the rules seems par for the course.
Its also implied she learnt some of this from the Bahro, who are likewise capable of breaking all manner of the things that the D'ni claimed were impossible. Best exemplified in that they are shown to be capable of writing a word, say "rain", which causes it to then begin raining.
In the Castlevania series, its revealed in the chronological first entry that Dracula became a vampire and started all his shenanigans because he obtained (or created?) the Crimson Stone. This is all fine and dandy, however while the director covered a few unexplained aspects of the series there have been no attempts made to officially explain why human malcontent and evil revives him whenever he is offed (or why this evidently happens like clockwork every 100 years, though he is "prematurely" revived about every 15 minutes), why he is in command of the Angel of Death (The Grim Reaper betrayed one vampire lord guy and gave his soul to Drac, evidently because he has the Crimson Stone. Nothing has ever stated why the Stone - if that's the reason at all- makes Death Drac's "confidant"), why the titular Castle of the series vanishes and reappears whenever Drac is out of his coffin, why he has apparent command over all the demons of hell and mythological creatures from every corner of the world, why he can enter what one game introduced as "The Chaos Realm" and exactly what this has to do with him (fan speculation is its the source of his powahs), or how exactly he went from being just a really powerful, pissed off vampire to becoming the "Dark Lord". We are left to assume that the Crimson Stone did all of it; while crafted through alchemy it may as well be wizardry.
In Team Fortress 2, Medieval Mode is an alternate game mode in which players are restricted to using "medieval" weapons and speak in Ye Olde Butchered English. Why? Because the Soldier angered a wizard. This doesn't explain the fact that the castle in which the game takes place is actually a high-tech spy base in disguise.
Later, that same wizard—who turns out to be the Soldier's roommate—is angered again and summons MONOCULUS, a demon possessing Demoman's other eyeball. The Halloween 2011 update revealed they're both pretty sucky roommates.
Then again, the wizard. In a comic released during the 2011 Smissmas update, Miss Pauling asks the Spy how the Soldier became a lawyer. Then the Spy replies: "His roommate is a magician. Should I continue?"
And in the 2012 Halloween Special, the wizard (named Merasmus) effectively gets pissed off at his roommate, stops living with him, and proceeds to attack the entire TF2 team for the length of his temper tantrum.
In Dragon Age II, when you hand over the Deep Road maps to Bartrand for his expedition, he asks you how you came by the maps. If Anders (the mage from Dragon Age Origins: Awakening, who gave you the maps in the first place) is in your party, he will quip, "A wizard did it." (Which is technically true, Anders himself being the wizard who did it, i.e. stole the maps.)
In Gear Head, a Roguelike with Humongous Mecha, the Noob Cave is an abandoned mine. The dungeon is character-scale (meaning, you go in on foot rather than take a mech, and the monsters are at your size), but in the character-scale mining elevator at the bottom of the mine, there's a Wolfram mining mech with the keys in the ignition, which you get upon returning to the surface. Quoth Word of God when questioned on the subject: "[The Wolfram] can fit in a subsurface mine because it's an enormous sci-fi megaproject and a wizard did it. ^_^"
Korol has a character who IS the Wizard who did it. He isn't even given a name - he's referred to as 'The Wizard' for the entirety of the game.
The goatmen or Khazra from the Diablo series turn out to have been created by the Vizjerei by magical corruption of captured umbaru tribesmen, and their previous lore as demonic lieutenants of Baal, the Lord of Destruction, turns out to have been nothing but Vizjerei propaganda meant to cover up their misdeeds.
The Fire Emblem series Zig-Zags this with regards to how Mages can move unhindered in desert terrain. Path of Radiance suggests the spirits they command literally part the sand in their path, while Heroes of Light and Shadow say it's simply bacause they wear light clothing.
In all fairness, the man who made the former claim was also noted, in the same sentence, to be a master bullshitter.
Happens in Penny Arcade Adventures Episode 4, wherein Gabe asks why the lands of Underhell is not falling when there is nothing to support it, the answer is simply that a wizard did it.
Another literal example, this time in Kingdom Hearts: In the Atlantica level in the first game and Chain of Memories, fire and lightning spells work underwater. But then again, they're spells...
A pretty apt description for somebody who completely fucks with the universe for his own convenience and/or amusement- an "omnipotent jackass" as Black Mage puts it. His otherwise-inexplicable cosmic jackassery includes, but is hardly limited to: shortening days from thirty-six hours to twenty-four hours just to make people hurry faster, bending time so his dinner will be done before he has to cook it (rewriting history in the process), dropping the entire continent of Australia on Black Mage, and crafting a spell designed to make Black Mage (and only Black Mage) vomit out his own organs. If anything in the world of Final Fantasy I just doesn't make sense, Sarda is somehow responsible.
Australia didn't actually exist in this version of the universe, as Black Mage's first comment upon noticing the sign with "welcome to Hurt, Australia" on it was "... and what's an Australia?"; and since our Earth was only in the prehistoric age at the time, as shown in an earlier strip, Sarda actually pulled the entire continent out of time and space just to fuck with Black Mage.
"Yeah, 'omnipotent jerkass' pretty much covers it."
This episode is titled "The Wizard(s) That Did it". Aptly titled, as multiple wizards are doing quite impossible things in it.
Essentially, once Black Mage stops being a Cosmic Plaything and Red Mage grows some sort of logical intelligence, these two will mostly likely become the new Wizards That Did It for this universe. The Universe is probably very unhappy with this arrangement.
In The Adventures of Dr. McNinja, Gordito asks Dan McNinja how the latter was able to take a bite of a bagel without removing his ninja mask. After giving a dead serious explanation for why he must never reveal his face, Dan blithely states that he uses "some ninja tricks" to eat while masked. In the Alt Text, Chris Hastings comments, "Any further questions regarding the McNinja's masks can be filed under 'ninja tricks.'"
In the AD&D-based Monster Manual Comics by Lore Sjoburg,  the strip on owlbears has the crew meet the actual "insane wizard" most of the peculiar early D&D monsters were blamed on — plus a guess as to his motives for doing so.
In the comic Skin Deep the characters transformation from human to their natural forms are explained as "Magic. Strong magic". Interesting case as the characters themselves admit they have no idea how that works. Asking them to explain the process is like asking someone how a television works. They know how it works, they just don't know how it works.
In Archie's Sonic the Hedgehog, Doctor Robotnik complains about how everything the Chaos Emeralds do is explained away by them being Chaos Emeralds. Snivelly points out that he uses them all the time, and Robotnik replies along the bounds that just because he knows they work doesn't mean that he has to like it.
Dragon Ball Multiverse: The author doesn't bother to explain how Buu's egg can enter into Babidi's ship through the door, and invokes this trope.
Hellfire Comm's Let's Play of Sonic 06. When asked by FTA to explain things like plotholes, magic mirrors, and all sorts, NTom64's answer is almost always "Magic" and that you shouldn't "come to him to question the logic of this game, as there is none."
Dark Magician Girl: Dark Magician, how come we can talk in this movie?
Dark Magician: A wizard did it.
The Binder of Shame. The aptly-named Killer DM Psycho Dave just had a player character hit by a random magical effect in his sleep just to mess with the player, and said character woke up to find his head had been turned into a giant piece of broccoli. When challenged to explain how and why, Dave replied "It's magic, I don't have to explain it."
Plinkett of Red Letter Media really hates "The Force Did It" or that Palpatine was deliberately planning everything to turn out exactly the way it did as the all-encompassing answers to plot holes and contrived coincidences in the Star Wars Prequels.
Plinkett: Oh, wait. I guess Palpatine was the guy that initially suggested the idea, so he might have been, like, using a trick on 'em or somethin'? You know, his grand plan was to butt all their judgement and trick them into letting Anakin go with her because he knew he was going to fall in love, get Padme pregnant, then have premonitions of future pregnancy complications resulting in her death, so that Palpatine could tell Anakin that he can use the dark side to save her so that Anakin could become Darth Vader and help Palpatine to rule the Empire. You'd think if this guy could see that far into the future he'd just pick the Lotto numbers.
Celestia: You two were so busy fighting you forgot to get any of the leaves down. Applejack: What are you talking about? We were kicking the trees and everything, how did we do the worst job?! Celestia: Because, uh... magic.
In "Chicken! Run!", Sweetie Belle acts as a Self-Backing Vocalist for an impromptu live performance. When asked how she sang both parts at the same time, the answer is "Magic!"
In Gravity Falls, Mabel believes a wizard is what made Dipper grow. Hilarity ensues. In actuallity, Dipper found magic crystals that can make things grow... Or shrink.
In the South Park episode Sexual Healing; the government suspects that the origin of sex addiction is from a malevolent Alien Wizard.
Very literally played in Shrek. Fiona's situation is explained only as "It's a spell. When I was a little girl, a witch cast a spell on me." That's all they bothered to explain her premise with, and it's the primary foundation of the plot.
Until the second movie at least. Even before then, the DVD extras made it pretty clear that's how Fiona naturally looks, the spell was what made her look normal. The Hand Wave was probably done because going into detail about what the witch did and why would have spoiled the plot.
In the Transformers mythos, it's Vector Prime's job to keep the timelines stable, so presumably any nitpicks are things he just didn't get to soon enough in relative time.
Also, in Transformers: Cybertron, the death of Unicron, resulting in the Unicron Singularity, is used to explain inconsistencies in the timeline. After all, when you kill a dark god, you really ought to expect something to happen to the fabric of the universe.
This is no doubt to cover up the fact that in the original Japanese series, Energon (SuperLink) was a sequel to Armada (Micron Legend), and Cybertron (Galaxy Force) was intended to be a third series in the same continuity, but (in Japan, at least) it was made its own series relatively late in development, leading to mass inconsistencies with the existing story and characters in its US adaptation, where it was kept as the third series in the so-called "Unicron Trilogy".
Not only that, due to the multiversal nature of the Transformers continuities, the Unicron Singularity can be used to explain away every inconsistency and plot-hole in every Transformers continuity EVER.
In Samurai Jack, all the characteristics of the future dystopia Jack ends up in are explained this way. Since the evil wizard Aku took over the world after he sent Jack to the future, he's the one responsible for the state of it. There are aliens on Earth? Aku opened up portals to other worlds. Robots are everywhere? Aku used magic to advance technology for use in his world conquest. And so on.
Kevin Spencer. When Kevin dies, his parents ask the wizard living in their back yard to bring him back. Percy repays the wizard by telling him to get off his property.
In My Little Pony: Friendship Is Magic, this is basically played straight by creator Lauren Faust in the form of "A Unicorn Pony Did It." Can be seen in this interview with her. When questioned by either new fans or people who are unfamiliar with the show how vehicles move or tortoises are given the ability to fly with a propeller harness, well versed Bronies will simply respond with "Magic."
To a certain degree, there is also "Because Pinkie Pie," referring to Pinkie's apparent ability to transcend dimensions, ignore physics, and ignore the Fourth Wall. Also, in the episode "Magic Duel", Pinkie Pie playing ten instruments is hoofwaved by Twilight Sparkle as: "That's not magic, that's just Pinkie Pie!"
In Real Life, this trope is also known as God of the gaps, only replacing the wizard with God (it's the habit some people have of handwaving everything, especially mysterious and unexplained phenomena not yet explained by science, by invoking God and leaving it at that without further reasoning or explanation). note But because of Rule of Cautious Editing Judgement, it's better to go with the Wizard. Note that the term itself is meant to be derisive; it was coined by Christian philosophers opposed to this approach. Some people replace "God" with "aliens".
Isaac Newton, famously, asserted that God had to periodically intervene in the universe to keep it stable, which may well be where the phrase originates.
It was customary for Christian thinkers and scientists to also attribute phenomena that could be explained to God, making "God Did It" the Mathematician's Answer to everything.
In this lecture, the speaker makes note of this kind of phenomenon whenever scientific findings are not given a proper theoretical explanation. The phrase "a wizard did it" is uttered multiple times to portray this.
Leonardo Da Vinci and Charles Babbage, though in the latter's case it's often more of a case of The Government Did Fund It, as the Analytical Engine (planned, but never built in Real Life) is usually the only thing he contributes.
Archmedes, Heron (of Alexandria), Copernicus, Roger Bacon etc., or you could even just say it was developed by an unnamed Babylonian/Hellenic/Arab/Chinese genius whose name is lost in the mists of time. The last one is the most justified and rational way to do it, as we'd naturally know more about the inventions and limitations of real and famous historical people, and there must have been any number of real instances (within reason) in history of this kind of thing occurring.
A common tactic of Conspiracy Theorists when trying to explain away certain flaws in their arguments is to say "they are the government and they're that powerful." Making the government in essence "the Wizard that Did It".
"As if by magic" is another related phrase. It's most often used in situations in which everyday gadgets are too complex for most people to take.
In Battle Master glitches, player absence, cheating, and other instances where out of character events effect the game it is usually hand waved as some mysterious magical incident.
This was essentially the origin of the Alien Space Bats trope in the Alternate History community- it was originally intended as a joke, implying that the only way certain implausible/ill-thought-out alternate timelines could happen was by some obscure outside force interfering in human history, like intervention by Sufficiently Advanced Aliens.