Factual error: As the X-Men land in Cairo, scenes reveal the destruction Magneto is wreaking around the world, where it is simultaneously daylight in New York, Sydney and Cairo - it is possible for it to be daylight in two of these locations at once, but not all three. (01:46:00)
Factual error: When Apocalypse touches the television in Cairo and says he is "Learning", the next shot shows the rooftops with many smallish satellite dishes in view. This is set in the early eighties when satellite dishes for TV were much larger.
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.
Suggested correction: Perhaps it happened 2 (or more) days ago, and Charles misspoke. Charles is tongue-tied in this entire scene because he is so smitten with Moira. He misspeaks in that very sentence. He says "I was - we were - hoping that you would tell us what happened yesterday in Egypt." He appears to be more concerned with concealing his feelings for Moira and probably didn't notice he said "yesterday."
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.
Revealing mistake: When Apocalypse first introduces himself to Magneto in the factory and tries to persuade him to join his side, a seam in Apocalypse's facial prosthetics next to his mouth is starting to come apart during a close-up shot.
Continuity mistake: The length of Eric's beard changes when he gets his new powers from Apocalypse.
Continuity mistake: While Eric is talking with Xavier beside Apocalypse and the others he takes a few steps but suddenly he is 60 feet away.
Continuity mistake: After Apocalypse pins Quicksilver to the ground, while he is holding Raven the space between them changes between shots.