Continuity mistake: There is a scene where the Chipmunks and Chipettes are singing the song "Girls of Rock and Roll." In that scene, it shows the boys walking up the stairs together and from left to right the order is: Simon, Alvin & Theodore. The shot goes to the girls then back to the guys. The order of the guys has switched: (left to right) Theodore, Alvin & Simon.
Continuity mistake: In the beginning when the photo of the Master is broken, the pieces of glass change position and then disappear altogether.
Continuity mistake: The BET is shielded by a metal dome that folded up. Nemesis Enforcer walks up and peels two portions back to reveal it inside the dome. Two shots later from the side, the dome is suddenly completely gone on that side, despite Nemesis Enforcer only peeling back a little of it. (01:08:30)
Continuity mistake: When George's wife asks him what made him drive all the way out here, their car is on the back of a large dinosaur at that moment. When it cuts to a closer angle for his reply, suddenly they are on a dirt road.