Continuity: When April puts her sword up after she cuts through some plants, the sword handle is next to her left shoulder. When the camera angle changes, the handle is next to her right shoulder.
Continuity: While April is going through the jungle in the beginning, she sticks her sword between her backpack and her back. However, the sword keeps disappearing and reappearing, and/or keeps changing sides.
Continuity: When Michelangelo enters the Turtle's lair, he throws his skateboard to the ground near the front entrance before descending down a stairway. When he goes to sit on the couch, his skateboard reappears laying on the floor by the platform but earlier shots has clearly shown it was not there before.
Continuity: In the scene where Mikey, Donnie and Leo go to April and Casey to get Raph, when Raph gets up there's no bandage on his arm. In the next shot, a closer shot just as he's sitting down, we can see that there's gauze wrapped around his arm.
Revealing mistakes: After Raphael argues with Donatello, and Splinter is introduced, Raphael's bandanna briefly turns grey as he leaves.