Other mistake: The crest of the clone trooper's helmet, when he points out that the cannons are being destroyed, does not reach down to the eyeslit, whereas it does with the others'.
Other mistake: Pleakley reacts to Jumba's "Where is my experiment?" too early.
Other mistake: Tails automatically knows Cosmo's name even before she introduces herself later on (English Dub version only).
Other mistake: Beast Boy and Wildebeest fight in a cage suspended in an endless room, with no solid ground underneath. But during the fight both combatants keep stepping onto the gaps formed by the cage bars without their feet falling through, as if the cage bars on the bottom side are merely painted onto a solid surface. For instance, watch Beast Boy's feet when he turns into a skunk.
Other mistake: In the scene where Raphael and Michelangelo report from their ceiling vantage point, we see a hallway full of Foot ninjas. Strangely, we can see a brief shot of an Earth Protection Force trooper walking peacefully among amongst the Foot even though they are hostile to them. (00:07:50)