User blog comment:Captain alex/My review of X-Men: First Class!/@comment-4043684-20111003232406/@comment-61371-20111003233858

Actually, Magneto's been an X-Man at least twice, and actively worked with Xavier to found the school before leaving for the exact reasons they parted in the movie. And Mystique was an X-Man as well, serving briefly after M-Day. As for the founders, you have to keep in mind that Storm, Colossus, and Nightcrawler were considered for the original team, but it was decided they'd be too hard to accept (see Uncanny X-Men #309 for that discussion), and Sage was used as a covert agent.

And, really, you have several alternate realities where the original X-Men weren't the same, and where Magneto stayed on with the school after its founding. You can't expect things to be the exact same across every interpretation. That just leads to stagnation.