Factual error: When Stryker's chopper with the mutants on board flies over the lake it enters a tunnel that barely clears the rotors. As any student pilot could tell you, this would lead to an immediate crash as the downwash from the rotors struck the bottom and sides of the rounded tunnel and reduced lift to zero.
Other mistake: Moira finds the ruins where Apocalypse is being revived in Egypt and it's the middle of the day, while it's night time in New York. Then when Xavier talks to her about it back state side, he mentions that it happened yesterday. It's a 15 hour flight alone just to get back.
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.