His claws originally appeared to be part of his glove, so the revelation that they were part of his body may or may not be considered a retcon. Later X-rays of his arms clearly showed that the claws were implants with mechanical housings and an extension/retraction mechanism. Later stories (as well as the cartoon) went with this and established that his claws are not affected by things that neutralize superpowers, even though his other powers are. When it was later "revealed" that his claws were a natural part of his skeletal system, the conflict with the earlier x-rays was never mentioned. (This includes his original entry in The Official Handbook of the Marvel Universe.) Similarly, Wolverine's eternal rival Sabretooth first appeared in Iron Fist as a psychopathic human murderer who wore clawed gloves.
Wolverine: The Jungle Adventure implies Apocalypse was involved in the Weapon X program, and that Logan has a child in the Savage Land. This has not been addressed since.
Logan: Path of the Warlord is set during Logan's past in Jasmine Falls.
New X-Men revealed Weapon X was but one project of Weapon Plus, masterminded by John Sublime. The Super Soldier program that lead to the creation of Captain America, Project Rebirth, was also a project of Weapon Plus.
Origin establishes Wolverine's name is James Howlett, born in 19th Century Canada, from an affair by Elizabeth Howlett and Thomas Logan. Dog Logan is James' half-brother.
The backstory of Bucky Barnes as the Winter Soldier affected Logan's past by having the Winter Soldier introduce and kill Logan's love Itsu during a mission in Jasmine Falls during the 40's, establishing the backstory of Logan's son Daken. This would have lasting repercussions for Logan.
Wolverine volume 3 and 4, Wolverine: Origins, and Wolverine: Weapon X Files establish Romulus as the main villain who has been messing with Logan for most of his life, just as Wolverine's son, Daken, was retroactively introduced.
Wolverine's Expansion Pack Past has included Logan being part of D-Day during the Normandy invasion and the liberation of the Netherlands, a prisoner at one of the Nazi concentration camps who used Gaslighting against a series of the camp's directors until they were each Driven to Suicide, and being a prisoner in Nagasaki on the same day the atomic bomb was dropped.
Sabretooth Reborn reveals Romulus was lying about Logan's Lupine origin, M-Day didn't restore all of Logan's forgotten memories, and that Logan remembers he volunteered for the Project X/Weapon X program after defeating members of Department H.
Sabretooth & Mystique's relationship. In the 90's it was revealed she & Sabretooth met in Germany while she was impersonating a woman named Lien Zauber. They had an affair and conceived a child, Graydon Creed. Sabretooth had no idea Zauber was really Mystique & Mystique faked her death to leave Sabretooth. When we see them interact, it's shown clearly that they don't like one another. Sabretooth hits on her a few times, but he also hit Pyslocke, whom he gutted & almost killed. Along with hitting on Jean Grey, so that doesn't count for much. He's almost killed Mystique on 2 occasions, and she in turn has poisoned him, talked down to him, played mind-games on him, and shown to find him so repulsive that she threatens to hurt him should he touch her. Fast-Forward to 2010, they were made Marvel's New Villain Couple during Jason Aaron's X-run, and were oddly affectionate with each other. They shared passionate & tender kisses, and Mystique's pet-name for Sabretooth is "dearest." Rick Remender seems fond of the relationship & kept it going in anything he wrote for the X-franchise. He even went so far as to retcon their first meeting in Germany. During AXIS, Mystique mentions their first meeting as them almost killing each other before they ravaged each other. She then cups Creed's face affectionately, and he tenderly holds her hand while they look at one another lovingly. A HUGE change from their disgust with one another in the 90's.
Samuel Guthrie, Cannonball, was revealed to be an immortal known as an External, and was recruited by Cable specifically to take down Apocalypse. After Selene defeated the Externals, she revealed Cannonball was not an External. In his own series, Cable went on to fight Apocalypse by himself, ignoring Cannonball's status as The Chosen One to take down Apocalypse.
Reignfire appeared in X-Force #26, and was intended to be Roberto da Costa from the future. But then it was explained that Reignfire was really the result of a scientist's experiment with a protoplasmic organism that used Roberto da Costa's genetic material as a template.
X-Force #46, #54, and #61 attempted to explain Shatterstar's true identity as another person named Benjamin Russell, but this plot point ended up as an Aborted Arc.
X-Force #102-105 reveals Pete Wisdom wears an eyepatch not because of an eye injury, but just to look cool.
So that one team member wouldn't end up committing Genocide, Jean Grey was rewritten so that she was never Phoenix and she never died on The Moon. It was the Phoenix Force itself, who took on Jean's appearance and memories (Quasi-confirmed in a later issue of What If..? which showed what would have happened if "Jean" had had her powers stripped rather than committing suicide). Has been retconned several times since then, the latest version is that it was Jean on the Moon. How she ended up in Jamaica Bay a few years after that isn't accounted for. Plus becoming Phoenix in the first place was a retcon. Xavier basically went "Oh, she had this powerful other self in her the whole time, that I just sealed away."
From an X-Menfan-parody film on Magneto's retcon survival: "No, that was actually Xorn's twin brother possessed by the sentient mold Sublime, pretending to be me, pretending to be Xorn." As crazy as that sounds, the parody writer is not making that up.
Beast: That defies all logic!
"Hey guys, there was a secret team of X-Men that I, Professor Xavier, sent off to their deaths. I really didn't mention it before because I thought that it would have been far too depressing for you guys, and because I am the biggest bastard on the planet. Now go on out there and save that world that both hates and fears us!"
X-Men: Deadly Genesis seemed like it was designed for the sole purpose of smearing Professor Xavier's reputation. For that matter, the writers have gotten a lot of mileage out of having Xavier do something shady in the past then wipe people's memory of it, even though this itself is a retcon of Xavier not believing in using his powers that way.
Magneto: Testament establishes Magneto's real name as Max Eisenhardt, with Erik Lehnsherr being an alias.
In issue 5 of Ultimate X Men, Magneto mentions his entire family dying in one of humanity's periodic genocides (alongside a background image of concentration camp prisoners in The Holocaust), a trait he supposedly shared at the time with his mainstream counterpart. On the other hand, issue 26 has him claim to be descended from a wealthy American family with whom he'd since parted ways. Then in issue 3 of Ultimate Origins, it's shown that neither applies: he was the son of two Canadian Weapon X agents, both of whose deaths he was responsible for, and was a young man in the '80s to boot.
Psylocke's Race Lift from a Caucasian British woman to a Japanese assassin was originally explained by Claremont as being the result of magic and surgery performed on her by Spiral and Mojo. After the title changed writers to Fabian Nicieza, he had not been aware of Claremont's explanation and introduced the character Revanche, who was said to be inhabiting Betsy's original body. In his version of events, Spiral and Mojo performed a body-swap on the two women, although he'd later state that their DNA and appearances became intermingled due to imperfections made in the swap. An initial earlier explanation by Nicieza had also stated that Kwannon had accidentally swapped her mind with Betsy after encountering her body on a beach, but this was retconned as false memories due to the inconsistency with what was shown when Betsy originally emerged from the Siege Perilous. note The details behind Psylocke's transformation from Uncanny X-Men #256-258 are revealed in X-Men #21-22, as the X-Men discover a scroll that turns out to be Kwannon's diary. But it turns out this explanation was not accurate enough, as issues #31-32 reveal the diary was a fake diary written by the crimelord Nyoirin.
In the late 90's, when Chris Claremont once more began writing for the X-Men, the character Sage was retconned to being one of Xavier's original students, placed as a spy in the Hellfire Club under Sebastian Shaw.
For a long time Rogue's stripe of white hair was explicitly dyed however it was later retconned to be natural.
After Age of Apocalypse, it was revealed Dark Beast and Gambit were retroactively responsible for the Mutant Massacre.
Onslaught reveals Xavier's attack on Magneto during Fatal Attractions created Onslaught, and that the X-traitor message, that motivated Bishop to travel to the past, was caused by Professor Xavier becoming Onslaught.
The Twelve revisits The Twelve storyline introduced in X-Factor, but the list of twelve mutants has been changed from the original story.
X-Men: The Hidden Years adds stories to the original run, and includes cameos by The Lost Generation's First Line. Professor Xavier and the X-Men and X-Men: First Class also add in stories during the original series leading up to Giant-Size X-Men.
Magma was originally the daughter of a senator of Nova Roma, a Roman colony established in South America that lived on long after the original Roman Empire died out. But in New Warriors, Fabian Nicieza felt it was impossible a place like that could exist without being discovered and so related that Nova Roma was created by the immortal sorceress Selene, who kidnapped and brainwashed people to revive a time period she had loved. Magma was said to actually be Alison Crestmere, the daughter of a British diplomat. But when the character returned in Xteme X Men, it was indicated that the "Allison Crestmere" identity was a fraud and she really was from Nova Roma. Further appearances (and inconsistent character changes) have muddled her into a true Continuity Snarl.
Adventures of the X-Men #12 reveals this particular 90's X-men inspired reality is the precursor to Earth-616. Because M'Kraan Crystal.
New X-Men reveals Charles Xavier had a sister, a Mummudrai spirit taking physical form that became stillborn, surviving to become Cassandra Nova. It's also established mutants can have a secondary mutation, such as Emma's diamond form.
Chuck Austen's run, including The Draco, establishes Nightcrawler and Angel are the descendants of the Neyaphem and Cheyarafim, with Azazel being Nightcrawler's father. Also, Angel's blood has the power to heal.
Uncanny X-Men #435 reveals the She-Hulk that slept with the Juggernaut was a tourist from Earth-721, known as Earth-A.
In First X-Men, Logan helps Charles Xavier form the X-men, establishing the Astonishing X-Men era mansion. Logan's team consists of Sabretooth, and the newly introduced Bomb, Holo, Meteor, Scout, Shadowshift, and Yeti.
X-Men: Giant-Size reveals shortly after their first mission, the X-men encountered the Evolutionaries.
X-Men (2019) reveals Moira to be a mutant with the ability to resurrect into a past version of herself, and that eight versions have died previously.
on Magneto's retcon survival: "No, that was actually Xorn's twin brother possessed by the sentient mold Sublime, pretending to be me, pretending to be Xorn." As crazy as that sounds, the parody writer is not making that up.