Plot hole: Although it is explained how the chipmunks were able to get away with the balloon race by tricking Ms. Miller, wouldn't Ms. Miller know that the chipettes were in on the balloon race? Especially considering the fact that she is their guardian? Also, why would she offer to babysit the chipmunks if she has chipettes to look after herself? Despite this, the chipettes were never brought along to Dave's house with Ms. Miller. And what is Ms. Miller still doing in Dave's house if she thinks the chipmunks are with Dave? Unless maybe she's taking care of the house...
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)