Continuity mistake: In the scene near the end where Ajax has a knife in the side of Deadpool's head and is punching him, later Deadpool pulls the knife out. In a follow up shot there is no hole in the mask where the knife was, but in a later shot the hole is there.
Continuity mistake: During the last great battle with Apocalypse, Beast hurls an entire automobile at Storm, and she recoils in fright. Before the car crushes Storm, Psylocke slices the automobile in half, with the two halves separating by several feet (at least 10 feet) before the shot changes. But in the next shot, the two halves of the car crash down on either side of Storm, separated by only a couple of feet.