Xavier & Magneto together at the start of X3
I don't thunk they're ignoring anything on this one.
We've seen Prof. X going to visit Erik in prison after trying to murder one of his students.(Rogue)
We saw them continue to be friends after Erik tried to booby trap Cerebro.
So it shouldn't be of much surprise that they would join forces again in the future.
They still could have recruited Jean & rebuilt Cerebro.
Xavier walking in said X3 scene and in XO:W