They still have many problems with X-men 1 and X-men 3 involving Prof X and Magneto still being friends in the 80s when they recruited Jean Grey, Magneto and Professor X knowing each other at the age of 17 (so roughly the 1950s), Magneto help building Cerebro, yet those two are at war between the 1960s to 1990s.
Either they are going to need more retcons or they are going to need more alternate universes/time travel to have everything make sense.