Continuity mistake: At the end, when Teddy and his friends get the directions to the Wizard's fortress, Prince Arin's hair is bright yellow as he shakes Wooly's hand. In the next shot it's back to his normal orange hair.
The Catwoman from Channel Six - S2-E12
Continuity mistake: Shredder thinks, "Those idiots have learned their lesson," so he transports Bebop and Rocksteady back to his lair. Bebop's wristwear switches to opposite sides; the chain bracelet is now on his right wrist, and the studded wristband is on his left wrist, then both return to their proper wrists. This happens again when Shredder makes the crack about his cheap mutant labor.