Plot hole: Superman traps the supervillain (whose power depends on sunlight) inside of an elevator to incapacitate him. Superman then ripped the elevator out of the building. He then plants it on the far side of the moon. Later on, sunlight starts to shine into the elevator through a slit at where the doors meet. The villain of course recharges and comes after Superman again. Now, if light could get through that crack there, then why couldn't it get through when the elevator was ripped out of the building in BROAD DAYLIGHT?
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)
Plot hole: Eagle catches and flies off with one of the cubs and Benji goes chasing after the eagle. After a bit of searching he spots what appears to be the missing cub but then Benji is chased by the nearby eagle before turning around to drive it off. But strangely Benji abandons looking for the fourth cub, as from this point forward we only see three cubs with him. This doesn't jive, as Benji has up to this point done everything to protect the cubs and keep all four of them together. (00:58:20 - 01:00:06)