The Wormhole wrote:
-Xavier's injurry during the final battle being what requires him to go in the wheelchair, despite the fact that we saw him walking in the flashback in X3 and his cameo in Wolverine.
I guess this is a case of simply choosing to ignore X3.
-Xavier and Magneto split at the end and Magneto turns villain, despite the X3 flashback shows them working together as recently as 20 years prior.
-Xavier and Mystique is one of those things that doesn't really contradict anything, but also just doesn't fit. They were so close growing up, and indeed there didn't really seem to be any bad blood between them when she chose to join Magneto, so why does she so willingly poison him in the first movie?
These two can easily be chalked up to the notion that "a lot of things can happen in 40+ years."