The movie steps on the toes of almost all the previous movies from a continuity standpoint. Matthew Vaughn claims that the prequels are actually part of an Ultimate Universe, though this has never been corroborated by any other official source.
- Xavier has his spinal injury at a much younger age than he apparently did in either X-Men Origins: Wolverine or X-Men: The Last Stand, and Magneto has his break with Xavier in the '60s before most of the characters from the other movies are even born, despite the scene in The Last Stand of him visiting young Jean Grey along with an noticeably elderly and mobile Xavier (not to mention Xavier getting his injury still with hair, while all his previous younger appearances had him bald and mobile).
- Xavier also initially gets Cerebro from the CIA and Beast rather than building it himself with Magneto, though that Cerebro is destroyed in Shaw's attack on the CIA, and a new one located at the mansion would have been needed anyway. note
- Magneto obtains the helmet from Shaw and Xavier is fully aware of how it blocks telepathy. In X-Men, Xavier is shocked at Magneto's helmet being able to block his telepathy.
- Regarding the Cerebro montage, Cyclops is a teenager in X-Men Origins: Wolverine (set in '79). James Marsden was born in '73 and in his late 20s filming the first two movies, but, if one does the math, he was actually playing a forty-year-old. Ditto for the girl made to resemble Storm, who looks like she's a teenager in this film.
- Charles and Erik briefly have a run-in with Wolverine, despite the original movie seeming to depict them meeting him for the very first time in the 2000's. Wolverine not remembering them is explained away by his memory loss at the end of X-Men Origins: Wolverine but it still creates the question of why neither Charles nor Magneto remember him or explain that they've met before. They only met for about five seconds, and they didn't even look him directly in the eye, so after over thirty years one can believe they might have trouble remembering him. And even in Days of Future Past, it took a while for Xavier to remember him.
- Emma Frost has a fairly significant role in X-Men Origins: Wolverine as a teenager, is now an adult 17 years earlier, in a completely different role, with additional powers, and playing for the opposite side. Xavier makes no comment about the resemblance when he sees her in X-Men Origins: Wolverine. note
- In X-Men, Professor X claims he and Magneto first met when the former was 17. This film has their first meeting in 1962, but prior to this shows a younger Charles Xavier aged around 11, alive and well in 1944.
- Hank McCoy becomes Beast in this film, but is shown on a television screen with a human appearance in X2: X-Men United, talking to Sebastian Shaw, who should look like Kevin Bacon and also should be dead by the 2000's. (Days of Future Past establishes that Hank developed a serum to reverse his blue furry form ... which he doesn't mention in Last Stand, when it's kind of relevant.)
- The discovery of the mutant gene is new (and eventually leads to America and Russia uniting to kill mutants) in 1962 in this film, but Congress is surprised and shocked by the existence of mutants in the "present day" of X-Men, which happens 40 years later.
- In this movie, it is established that Mystique and Prof. X grew up together. Seems odd that she would be so casual about attempting to kill him in X-Men and at no point did Charles express any real knowledge of her outside of being Magneto's lackey.
- Matthew Vaughn, director of the movie, stated he tried to fit with only the trilogy instead of X-Men Origins: Wolverine. Too bad Fox and the makers of said movie's Blu-Ray didn't listen, and the Cerebro bonus feature profiling most mutants try to put all 5 films in the same timeline (as mentioned above, Emma
◊ Frost◊ is the most senseless). - In the original trilogy, Xavier mentions that Scott, Jean, and Storm were his first students. According to this film, Days of Future Past, and Apocalypse, the three of them don't show up for decades after Xavier opens the school.
- The official comic book prequel to the first X-Men movie depicted Charles meeting Erik for the first time in Israel during The '90s, with both men being middle-aged and Charles already being bald. Here, they meet for the first time as young men in 1960's America, and Charles still has a full head of hair.
- During The Stinger, Erik rescues Emma Frost from CIA Headquarters, wearing a distinctive red outfit and red-tinted, horned helmet reminiscent of his classic comic incarnation (and seemingly adapted from the silver helmet he took from Shaw). While it's not out of the realm of possibility that he may have created more than one helmet, the distinctive silver helmet he wears through the entirety of the film is what he later chooses to wear for decades afterwards, right up until he is caught prior to the flashback scenes in Days of Future Past, and then subsequently through the events of Apocalypse and Dark Phoenix, while the red helmet he sports in The Stinger of this film is never seen again. It is also decidedly not the same helmet seen in X1, which is more rounded and doesn't have any horns.
