Continuity mistake: The end of the episode shows Xavier standing with no assistance. The only time in the series that the use of his legs were restored were a side effect of him losing his powers. He has his powers in this scene, so there's not really any reason for him to suddenly have the use of his legs back.
Other mistake: During the montage of people being erased from time, the exterior shot of the X-Mansion shows part of the mansion destroyed. The mansion is later shown to be destroyed by Graymalkin after the heroes defeat Apocalypse, but at this point in the episode there's no reason for the damage.