Continuity: In one episode, right when Donatello is talking to an outer space companion, he gains Michaelangelo's body.
Factual errors: In the episode "Enter The Rat King", the turtles are climbing up the Channel 6 building, Donatello says "I wish we had those anti-gravity boots from episode 6." He was referring to the episode "Sky Turtles." But Sky Turtles was actually episode 23. Episode 6 was "Return of the Shredder" which did not feature anti-gravity boots.
Continuity: In the episode "Return the Shredder" when the turtles arrive at Channel 6 and as soon as Michaelangelo says "What's the haps?" Raphael gains blue body bands.
Continuity: In the episode "Michaelangelo Meets Bugman" when Michaelangelo throws his grappling hook, the letter D (for Donatello) appears on his belt.
Audio/visual unsynchronized: In the episode "Return of the Shredder", when Leonardo says the phrase starting with "That same gel", it's coming out of Raphael's mouth.
Continuity: In the episode "Sky Turtles", Donatello suddenly appears in the driver's seat of the Turtle Blimp and talks like he's flying it, when in fact Leonardo was flying the whole time.
Continuity: In the episode "Hot Rodding Teenagers", the turtles' sitting arrangements in the Turtle Van change constantly.
Audio/visual unsynchronized: In many of the earlier episodes, a specific turtle's line would come out of the wrong character's mouth (i.e., Leonardo speaking with Raphael's voice).