Captain America has a few, usually retcons that fans will ignore:
The retcon that Sam Wilson was a pimp prior to be being the Falcon. It's disliked for being a needless retcon that darkens the character, while also being racist. It was ignored by pretty much every reader until Marvel eventually obliged in 2015, revealing that "Snap" Wilson was a false memory implanted by The Red Skull to try and break Falcon's spirit.
The latter part of Mark Gruenwald's run as writer, from around 1992, until 1995 when Mark Waid took over, post Heroes Reborn, is considered a giant Dork Age. Lowlights include "The Superia Strategem" (Where Cap and his male ally Paladin almost get transformed into women by the titular Big Bad), "Cap Wolf" (Cap gets transformed into a werewolf by a mad scientist. Wolverine and Cable both show up, because it was The 1990s) and "Iron Cap" (The Super Soldier Serum turns toxic, and Cap dons a ridiculous suit of Powered Armor to keep fighting).
Rick Remender's retcon that Steve Roger's father was an abusive drunk. It is disliked for being a stereotype of Irish immigrants while also adding nothing to the character aside from giving Steve pointless angst. It doesn't help that it was also a part of Nick Spencer's disliked run. Most people choose to ignore it, which is pretty easy given that Steve's father is so minor a character that most people would be more familiar with the MCU version — also a minor character — who isn't presented in this light.
The Marvel Civil War spawned a massiveAudience-Alienating Era, what with Robbie Baldwin ditching his Speedball identity to become the Wangsty Penance because of an explosion that wasn't even his fault, Iron Man becoming a major-league Jerkass, and Spider-Man willingly unmasking himself on national television. Hence, some fans have decided that Civil War never happened. There was a fan parody called "I Don't Need Your Civil War," created from leaked pages for some aborted project or other. The reasoning behind the name is a Shout-Out to Guns N' Roses.
The assumption of Fanon Discontinuity has become so prevalent that many Marvelverse fanfic writers don't even bother to add a disclaimer mentioning that the writer is ignoring Civil War in a particular fanfic, as it's pretty much implied.
Even its sequel story Civil War II fell into this for being a unwanted tie-in to Captain America: Civil War, being a rehash to the already divisive original, being published during the Black Lives Matter movement, Captain Marvel becoming a jerk and for the deaths of War Machine, She-Hulk and Bruce Banner, though for the middle, she turned out to be Not Quite Dead. It doesn't help that it ended the All-New, All-Different Marvel branding and beginning the 2016 version of Marvel NOW!. Hawkeye fans were very pissed at the scene in which he kills Banner. Not only that, the controversial ending where Captain Marvel puts Iron Man in a coma.
This whole Totem concept introduced by J. Michael Straczynski, which has been disregarded by many. Spider-Man did not get his powers from a spider-totem; Morlun suffered from a case of Mistaken Identity in going after Spidey; Spider-Man never died after getting his eye ripped out before coming back from the dead to eat Morlun alive; and he never got any new powers.
There was a period in the '90s where someone had the bright idea to get MJ on a plane and have her Killed Off for Real when it exploded; after the revenge-and-grief subplot was over and readers were told that she was really, truly dead, Spidey immediately became swingin' single - hanging out with his friends in clubs, having a new roommate, being flirted with by new women. It didn't work. The outcry prompted an Author's Saving Throw, MJ came back, and if the entire storyline happened at all, it was simply that there was a brief scare where she was thought to be dead.
A lot of fans refuse to accept the fact that One More Day exists. No, Peter didn't sell his marriage to the Devil. No, Mary Jane didn't agree to that either. No, Mephisto wasn't that petty to do something like that. And no, the Marvel universe isn't so dumb to the point that the most intelligent people on the planet and the world's most powerful magician can't heal a bullet wound.
Some fans will refuse to accept that Otto Octavius is now Spider-Man, and prefer to wait for the writers to bring Peter back from the dead. Well, as of the end of that series (and the beginning of the new Amazing Spider-Man series), they got their wish..
The oft-reviled Sins Past story involved the "reveal" that Gwen Stacy had a one night stand with Norman Osborn, and gave birth to his twins. Fortunately for the many fans who hated the concept, the twins were later revealed to be clones created by Harry Osborn prior to his death, who had hired Mysterio to hypnotize both Mary Jane and Norman into believing Gwen had cheated on Peter.
Insect DNA and the Queen.
Many of those who were at least receptive to the Totem concept were chased off by the series of backup stories in the post-Superior, Amazing Spider-Man relaunch (tying it with Spider-Verse), in which Morlun and his "siblings" bounced about the multi-verse devouring assorted versions of Spider-Man and slaughtering anyone else in their path. The last straw came in Amazing #8, where Daemos killed the Peter Parker of the MC2 universe. Many, fairly, saw that as yet another middle finger to the Spider-Man fandom. Fortunately, the newspaper strip universe was spared, and a back-up tie-in by Spider-Girl's creators hinted that the MC 2 affected by Spider-Verse was not in fact the real one. Unwilling to muddy the waters any further, Marvel ultimately caved in to pressure and resurrected the MC 2 Spider-Man, giving back a happy ending to at least one version of Spider-Man
The Gathering of Five/The Final Chapter. Aunt May never returned from the dead after her moving death scene in Amazing Spider-Man #400. Anything to the contrary was just Peter fantasizing about scenarios in which she might somehow still be alive, the way many of us do when a loved one dies. There's certainly no way Peter would have been fooled by a 'genetically re-engineered actress' posing as Aunt May - his Spider-Sense would have told him something was up. And there's no way the actress could have faked Aunt May's personality that easily, and no way would she have stayed in character even on her deathbed.
Worst of all, while OMD/BND would have been a perfect place to erase this from continuity... nope.
Considering how Zeb Wells' relaunch of Amazing Spider-Man undid a great deal of the hard work put into restoring the Peter/MJ relationship in the previous run, it's little wonder some fans consider Nick Spencer's run a jumping-off point with an all too rare happy ending for the wall-crawler and his favourite redhead.
Some fans of the Ultimate Spider-Man book dismiss anything after Ultimatium (or in Ultimatium, for that matter, as that storyline isn't liked much at all) to be non-canon. Peter and MJ didn't break up so Peter could be with Gwen, who initially viewed Peter as a "little brother" (which, to Bendis' credit, is pointed out by MJ), and Peter didn't die in the "Death of Spider-Man" story. Ultimate Spider-Man Annual #3, in which MJ promises to "totally marry" Peter one day, is often cited by some fans as the "true" climax of the whole story. This is somewhat rectified by Peter coming Back from the Dead and eloping with MJ.
Spider-Woman: Origin: The revised origin by Brian Michael Bendis is considered non-canon due to significantly altering details established in earlier stories, and for presenting Bova and the High Evolutionary as ordinary humans, when several stories depend on their established likeness being present (though the latter was somewhat ambiguous, and hinted to be Jessica's altered memories at work).
Due to the massively unpopular rewrites of canon history and the characters themselves, most fans of Malibu Comic's The Ultraverse tend to ignore the books written after Marvel Comics bought the rights to them in the mid-90s.
Doctor Doom has been through a number of unpopular depictions over the years, causing many fan rejections. Fortunately, the concept of the Doombot has already been introduced: Doom uses a lot of robots, some of which don't quite act right. This conveniently lets fans (and future writers who want to make an Author's Saving Throw) explain away any drastically inconsistent appearance of Doom as a Doombot:
Dr. Doom most certainly did not get his ass handed to him by Tony Stark's new team of fascism-abiding "Avengers" in a flagrant violation of international law against a sovereign nation, and to suggest that he was then subsequently imprisoned by said miscreants is just laughable. Such libelous poppycock is beneath Doom.
He also absolutely did not, at any time during this clearly fictional sequence of events, ever lapse into speech patterns whose vulgarity, crudity, and misogyny would have shamed both the intellect and character of your average gang-banging crack addict.
Hilariously, Doom himself is known to indulge in exactly this sort of historical revisionism. He keeps an official Editor on staff to remove or improve the records of all his embarrassing moments. The above items are probably that Editor's work.
He was beaten by Squirrel Girl, though. That was written by Steve Ditko! That's so in continuity!
Doom's 'Master Planning' also includes that racist Doombot from the Black Panther issues. Fans still aren't sure how that one made it past the quality control, but a racist Doombot has to be a part of Doom's master plan rather than some sort of twisted out of character moment on a horrible writer's self-insertion fantasy.
A lot of us try and make others wake up and smell the coffee in that DOOM would not make a Deal with the Devil in order to go after that infernal Richards, after what happened to his mother dearest. No matter what Mark Waid would think.
Another one is the story of Doom serving the Marquis of Death, being sent back in time by the Marquis for not being evil enough, torn apart by prehistoric sharks, surviving by pure hate, and somehow recreating his body, growing stronger in dark magic, and living for millions of years only to show up to kill the Marquis after the FF have defeated him. While the depiction of Doom's determination is fitting, since Doom would rather die than call anyone else master, along with the general ridiculousness of the storyline, the next one and all other ones have conveniently ignored it.
An issue of Dark Avengers several years later retconned parts of the story. Doom was heavily wounded by the sharks, but saved by the Dark Avengers, who were going through unrelated time travel problems. He hijacked their time machine to get back to the present and plot from there, establishing that most of the above story was a lie.
There was a Usenet meme: "Jean Grey is dead on the moon." The theory was that Jean Grey being resurrected for X-Factor, the retcon's effect on the original "Dark Phoenix Saga". Yet two wrongs don't make a right, and the Emma Frost thing doesn't sit too well with some fans either. Then again, Jean even dating Scott, letting alone marrying him, is Fanon Discontinuity for the Jean/Logan fans, so there seems to be a line where this goes too far and just makes for messy fanon.
Many things from Uncanny X-Men (Chuck Austen) are worth denying. Many fans agree to dismiss the following: Nightcrawler's father is not an ancient demonic mutant, nor does Nightcrawler have hundreds of similar-looking half-siblings running around that no one ever noticed. The Church of Humanity did not try to turn Nightcrawler into the Pope and then kill people with exploding Communion Host. There are no parrot wolves of doom. Warren Worthington the Third CERTAINLY knows what businesses he owns and would never bang some jailbait in front of her mom. Havok never offered to reform Iceman's body by peeing or fell in love with his nurse in his dreams. Sam Guthrie's family was NEVER in a bad Romeo and Juliet ripoff facing rednecks with super-armor. She-Hulk did not fuck the Juggernaut. Skin's tombstone didn't get his name wrong. There was no second Xorn. Mutants are not immune to AIDS, and let us never speak of that again.
Frankly, it's easier to list the parts of Austen's run that fans are willing to remember, which consists of "Juggernaut was an X-Man" and pretty much nothing else.
Grant Morrison as stated they deliberately wrote "Here Comes Tomorrow", the last story of their New X-Men run, in a way that it could be the last X-Men story if fans so chose. Ironically, though, given some of stuff they did on the book, including Emma Frost coercing a still-traumatized Cyclops into an affair while he was still married to Jean Grey, killing off Jean, and writing Magneto in a manner similar to his Ultimate self, some fans would rather take this approach to Morrison's run itself.
Some X-Men fans have had this reaction to Reginald Hudlin's work on the Black Panther comics, including the retconning of the nation of Wakanda so it's intentionally keeping high technology (including the cure for cancer!) from non-natives, and Storm stepping down as one of the leaders of the X-Men to marry T'Challa in the sake of a Token Romance. This relationship is sunk with a single line of dialogue in Avengers vs. X-Men.
Don't get X-Fans started on House of M and the Decimation that resulted. Wanda Maximoff's depowering all the B-list and lower mutants in the Marvel Universe simply by saying "No More Mutants" is just too ridiculous a Diabolus ex Machina to be accepted as canon, and it's a textbook case of Writer on Board. Many fans still curse Brian Michael Bendis' very name to this day.
And many general-Marvel fans go further by refusing to accept Avengers Disassembled, the arc that came before House of M. Though far from being the biggest problem with the arc, a good number have cited some of the author-induced sheer stupidity that Doctor Strange displays when he shows up as a reason, and this was one of the biggest things dealt with in the subsequent "What If..." story based on the arc.
Submitted for your consideration: The Crossing, The Avengers crossover where Iron Man is revealed to be a sleeper agent working for Kang, commits cold blooded murder and attacks his fellow Avengers. The Avengers desperate to stop their rampaging teammate recruit a teenage Tony Stark from an alternate universe to help them defeat his older, more experienced counterpart. This teenager then takes over the role of Iron Man and fights crime as the new Iron Man. Kurt Busiek tried applying Canon Discontinuity in Avengers Forever to wipe away this stain on The Avengers mythos, but it was totally unnecessary. Nobody at Marvel will ever admit to remembering teen Tony.
Though, there was one positive side-effect to the whole enterprise: it allowed Heroes Return to essentially restore Tony Stark back to what he was before The Crossing. More or less, anyway.
Avengers Arena. As far as Runaways fans are concerned, Nico and Chase are still in LA with the gang and are not fighting other teens to the death. A lot of Avengers Academy fans have a similar mantra regarding it.
Ditto for the sequel to Arena, in which they are joined by fans of Baron Zemo and Daimon Hellstrom, who did not appreciate the two popular Antiheroes being turned into one-dimensional leaders of a Neo-Nazi organization that framed Nico, Chase and Hazmat in a murder and forced them to join their group.
In the wake of Arena and Undercover and their general dissatisfaction with the second and third volumes, a number of Runaways fans now insist that the series ended after the original run.
Fans are split on a retcon of the Beyonder's nature; originally, he was a sentient universe in human form with nearly infinite power, but he was later revealed to "actually" be a Cosmic Cube Being, an entity of still-phenomenal power but a relative small fry on the cosmic scale. This caused a divide between fans who felt the original incarnation was an obnoxious self-insert for his creator Jim Shooter and those who felt the retcon was so sloppy (turns out the various Anthropomorphic Personifications were only pretending to be weaker than him) that they'd prefer to see him restored to his original power level.
Invoked in the final issue of Dan Slott's She-Hulk, which featured Alternate Universe counterparts of various Marvel characters going on vacation to Earth-616 and generally making a mess of things, with the strong implication that a reader could consider any given Character Derailment or Unexplained Recovery to actually have been one of these guys if they wanted to. The plotline was poorly-received, oddly enough.
Quicksilver and Scarlet Witch fans disregard the Retcon that they're not Magneto's children in AXIS as canon. Most of these fans figure that this will be retconned back once the X-Men movie rights revert back to Marvel, while others blame Marvel for retconning their origins to fit in with their Marvel Cinematic Universe counterparts.
There are Iron Man fans who disregard Tony's current origins in which he is adopted and not the biological son of Howard and Maria Stark by revealing that he is the son of Jude and Amanda Armstrong and there are fans who don't like the idea of Riri Williams as Iron Mannote Later changed to Ironheart after the fan backlash, as they consider her a Replacement Scrappy.
On the whole, most fans prefer to pretend the Carol Danvers/Marcus Immortus incident in Avengers #200 never happened. Marcus used mind control to drag Carol into his pocket dimension, seduce her, and impregnate her with a copy of himself. When she delivered the baby and it rapidly aged to adulthood, the Avengers foiled Marcus's plan to stay in the main Marvel universe. But then, when Carol announced she'd return to his dimension and live happily ever after with him, the team said okey-dokey. Chris Claremont fixed this a year later with something even better than a retcon: He brought Carol back and let her deliver a giantWhat the hell, heroes? lecture to the Avengers before quitting the team and going to hang out with the X-Men.
Jeph Loeb and Daniel Way's Wolverine run is considered a massively drawn-out Audience-Alienating Era and is ignored. Wolverine is not from a subspecies of mutants evolved from wolves, there's no super special genetic destiny showdown of the fates reason for his rivalry with Sabretooth and there's no jackass called Romulus who manipulated everything in Wolverine's entire life for vague reasons. The only thing acknowledged from the run is Daken, Wolverine's son, whose origin is heavily tied to all of the above... which writers thoroughly, thoroughly ignore and have never brought up again aside from vague references to Logan not being there to raise him and Daken having a cruel upbringing. The wolf mutant thing was also revealed to be a lie at the very end of the run, to the relief of all.
Thunderbolts ended on the 75th issue, was revived with the 18 issue New Thunderbolts, and then the name reverted for issue 100, even if that means there are certainly six comics missing. (as put in a way resembling what those comics were instead of the 'hero team made out of villains', "I’m gonna break Rules 1 & 2 and talk aboutFightbolts.")
Rose/Richard Fisk has been a fairly popular Spider-Man villain since 1972, typically depicted as a crime lord who prefers long-term schemes to actual violence. The 1992 story-arc "Name of the Rose" introduced several unpopular retcons in an attempt to revamp the character. The character acting as the Rose in the story turned out to be an imposter, while the real Richard Fisk re-emerged as a Punisher-like vigilante called Blood Rose who had no problem with setting occupied buildings on fire. The over-the-top violence and convoluted writing of the story were poorly received even during the story's original publication. The following appearances of Richard mostly ignored these changes to his personality and methods. Long-term fans of Spidey and his supporting cast tend to pretend that the "Name of the Rose" story-arc never happened.
You would be very hard-pressed to find a fan of Marvel that actually likes Thor: Vikings, which whilst published as part of the Marvel MAX line isn't explicitly in an alternative community like other MAX titles and which Garth Ennis himself has said is canon. Fans near-universally reject the idea of such things as New York City seeing tens of thousands of people slaughtered, tortured and raped by a crew of undead vikings, Doctor Strange hiding from said undead vikings in his illusion-veiled home like a coward, and Thor being completely incapable of battling said undead vikings on his own and instead having to summon three ordinary people from different points in time to fight the undead vikings for him up until the plot requires him to defeat their monstrous leader Haereld Jakelson on his own. Fortunately for the readers, every non-Ennis writer Marvel has seems to also refuse to accept this story as canon.
When Frank Miller originally introduced Elektra, she was depicted as someone who started normal before her father was killed, which set her on the path to become an assassin. Among the many things Miller changed when he came back for the Man without Fear miniseries was retconning that Elektra always had psychological issues, hearing voices and intentionally setting out would-be assailants to kill. Much like with Miller's changes to Catwoman in Batman: Year One, the changes to Elektra are regarded as a black mark on an otherwise well-regarded story.
Even for a franchise with dark roots since Miller's first run, even found the miniseries Daredevil: Father to be a bridge too far for them, mostly due to the revelation that the "kindly old man" Matt was blinded trying to save was anything but; he was molesting his own daughter — and said daughter becoming a revenge-obsessed killer going after Matt due to this.
.")