Marvel Comics' history is full of amazing, iconic moments. There are some cringe-worthy parts to it as well. So it goes with any franchise that's been going for the better part of a century. While DC Comics has continuously rebooted its complicated history, Marvel hasn't. That doesn't mean they haven't changed some things along the way, and not always for the better.
The retcon is inevitable in any long-running narrative. It's a storytelling device that when used to great effect can reframe a story in unique and positive ways. But sometimes it can lead to disaster, upending long-held beliefs (and facts), leaving fans frustrated and confused.
10 Sentry Could Touch Rogue
Rogue's entire character is built around the fact she can't touch other people without severe consequences. She absorbs superpowers, memories, and sometimes, a person's mind. So it was a little confusing during the funeral of superhero Sentry that fans learned she had an affair with him before he died. This sparked a lot of questions about Rogue and Sentry, namely why (and how). I never came up again, though. Relatively minor on the scale of retcons, this one still left fans confused.
9 Iron Man Was Evil
The 90s were not a great time for Marvel storytelling wise. The need for shock and awe reveals and twists got out of hand, as seen in The Crossing event that played out in the Avengers. Iron Man was revealed to be a secret agent of one of the versions of Kang The Conqueror for his entire Marvel career. He then proceeded to murder people with knowledge of this, utterly destroying the history and integrity of the iconic character. All of this too was eventually retconned away, like it never happened.
8 Gwen Stacy Had Twins... With Green Goblin
Sometimes retcons feel like a betrayal to fans because they completely undo long-held beliefs and perceptions about a character. Gwen Stacy occupies a special place in the hearts of Marvel fans, so it was confusing and upsetting when it was revealed that she had an affair with Norman Osborne, AKA Green Goblin, one of Spider-Man's oldest villains. Not only that, she had twins with him. This revelation cratered the understanding that Gwen had been a tragic victim of Green Goblin, instead of somehow complicit in his behavior.
7 Xorn Is Magneto
The history of the character Xorn is fairly complicated. The mutant with a supernova for a head debuted during the Grant Morrison New X-Men run in the early 2000s. Some aspects of the hallmark run have lasted, but some things, like Xorn, have been undone. Xorn was later revealed to be Magneto, who was previously thought dead.
This led to so much confusion among fans that it was later retconned again. It was revealed that the Magneto Xorn was in fact a twin of the real Xorn (that no one had ever known about). This didn't exactly clear things up, but Marvel quickly moved on.
6 How Doctor Doom Was Disfigured
Doctor Doom is one of the greatest villains of the Marvel universe. He has the best set of armor, except compared to Iron Man perhaps. Beneath that armor is a scarred visage few ever see. How he got injured was one of Marvel's weakest retcons. Doom blamed Reed Richards for his disfigurement, which occurred when Doom tried to travel to Hell to rescue his mother from Mephisto. He blamed Reed Richards for his suffering since Mr. Fantastic warned him it wouldn't work. Later retcons had Mephisto sabotaging the machine Doom used to travel, and then the Thing, muddying the water on the motivation behind Doom's hatred of Richards.
5 The Clone Saga
The entire Clone Saga in Spider-Man is a retcon inside a retcon. There were some good and bad elements to the Clone Saga, but it was ultimately a years-long ordeal that left Spider-Man fans confused and exhausted. First, it was revealed that a clone of Peter Parker created by the Jackal had survived. This was Ben Reilly. Then it was revealed Peter was in fact the clone (kind of). Then the whole thing collapsed into confusion as the writers piled more clones and sub-plots on to the story before ultimately retreating from the idea.
4 Peter Parker And Mary Jane Never Married
Another major Marvel retcon fans did not like also involved Spider-Man. The decision to handwave away Peter Parker and Mary Jane Watson's marriage like it never happened in the One More Day event proved one of the most controversial decisions Marvel ever made. Some fans argued it left all of Marvel continuity after their marriage in absolute confusion, while others didn't see the need for it at all. The retcon still sits uneasily within Marvel continuity, which has more or less remained intact while this aspect hasn't.
3 Tony Stark Is Adopted
The decision to make Iron Man a villain was controversial (as it was when Captain America turned out to be an agent of HYDRA). Also unpopular was making Tony Stark adopted. The main point of contention was that changing Tony Stark from Howard Stark's biological son to adopted son didn't really add anything to the story.
Also, how it came about was complicated and confusing. Howard Stark's wife Maria couldn't have children, so Howard contacted an alien who helped them conceive but the baby turned out evil and went to the future so they ended up adopted Tony.
2 Scarlet Witch And Quicksilver Aren't Children Of Magneto
Scarlet Witch and Quicksilver had long been established as the children of Magneto. This was undone when they discovered that they weren't his children or even mutants. The powerful twins were mutates of the High Evolutionary, a powerful cosmic being. This frustrated fans, but it did lead to their origin being revised in the MCU. To be fair, that had more to do with rights issues, but with the X-Men and Avengers back under one roof at Disney, it seems there could be a retcon potentially in WandaVision. Quicksilver is anticipated to be in the show, which could open the door to revising Wanda's parentage.
1 Jean Grey Didn't Die
One of the most tragic events in Marvel Comics' history occurred when Jean Grey sacrificed herself to stop the Phoenix Force. Her death was jarring and it seemed, permanent. But a few years later, one of the first major Marvel retcons occurred when it was revealed that Jean had actually survived. The Phoenix Force placed her in hibernation and then impersonated her, completely undoing Jean's growth and agency in her most important story. It set off a series of deaths and rebirths for Jean and the Phoenix.