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: After Lieutenant Falcon gets in trouble for bringing a date on base, the girl he brings is ordered away. She goes to a lake and strips off her white dress, showing off her one piece, and kicks the dress aside gently. In all the immediate shots following, when she's revealed as a Cobra agent and others are with her, the dress is nowhere to be seen. (00:33:10)
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.