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.
Plot hole: After being hit with the spores, Cobra Commander cannot walk or even move very well with any speed at all. The Cobra minions have to drag him to their prison with the Joes and just leave him there on the ground after the Joes make a break for it. The Joes go quite a distance to engage Cobra. Road Block is delayed only a couple seconds behind the other Joes when he is grabbed, but knocks out the minion who grabbed him. Suddenly, Cobra Commander is at his feet telling him to wait because it's a trap. Later, Road Block has to carry Cobra Commander because he still can't move much. There's no way Cobra Commander could have caught up with Road Block to warn him of the trap. (00:52:50)Quantom X