As this comic was published long before X-Men: The Last Stand and X-Men: First Class, it contained scenes which are not canonical with either film:
Charles Xavier first met Erik Lehnsherr in Israel during the year 1992, which contradicts Last Stand (where Charles and Erik were shown visiting a young Jean Grey "twenty years" before the events of the film) and First Class (where Charles and Erik were shown to have met in 1962).
Xavier and Magneto part ways after Charles tried to stop Magneto from murdering Hans Von Shank, the Nazi who was responsible for the death of Magneto's family. In First Class, Magneto left Xavier after Xavier prevented Magneto from destroying US and Soviet fleets, and in the process accidentally paralyzed Xavier while deflecting shots from Moira MacTaggert
