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.
Factual error: The Joes chase Cobra into the snowy mountains and attack inside the weird cave. One of the Joe's vehicles splits to a driving section, and Road Block flying up in a little fighter. Road Block is holding a large rifle with both hands, yet the fighter goes up and turns around and begins flying at his control but he never touches a steering wheel or anything. Just his big gun. And he does not speak so no voice commands are given. How is he flying with no hands? (00:19:40)
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.