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 opening battle sequence, Cobra Commander takes a bomb and sets it for 3:00 minutes. As he flies with his jet pack to the Statue of Liberty, it counts down to 2:58. He lands and places the bomb, and laser blasts hit all around him before he turns and flies off. This takes about 5 seconds to do, but the timer on the bomb stays at 2:58 for the full time of him landing, placing the bomb, and flying away. (00:01:35)