Plot hole: In their previous encounters with the Triceratons, the Turtles had to learn the hard way that the Triceratons breathe not oxygen but a combination of nitrogen and sulfur, which is detrimental to most Earth lifeforms, and thus had to wear special rebreathers. When the Turtles, Splinter, April and Casey enter Zanramon's throne room along with Traximus, none of them wear any breathing equipment to protect themselves from the hostile atmosphere.
Other mistake: When Hebi learns of the Mogura (mole) Ninja's failed attempt to capture their prime target, Lord Noriyuki, the Ninja leader who delivers Tomoe Ame to him speaks only of "interference". But when Chizu is called forth, Hebi commands her to deal with the kame Ninja (meaning Leonardo) even though his presence was not verbally mentioned beforehand.
Continuity mistake: Before the Turtles were carted off to the arena in the previous episode, they were disarmed. But once they have been confined to the gladiators' quarters, when Ralph asks about Traximus ("Who's Mister Sunshine?"), at that very moment he has his sai back in his belt.
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)
Continuity mistake: Nano fells the statue of Zippy Lad during his fight with the Justice Force. When the statue topples, the area before it is empty until it shatters. But in the next cut, we see Zippy Lad sitting in his wheelchair right before his own statue, with no debris lying around. It's simply the re-insertion of a previous cut, when Zippy Lad is criticizing the three failed applicants.
Continuity mistake: When the Turtles and the rest of the gladiators are to be ferried up to the arena, Gruel the overseer refuses to give back the Turtles' weapons. But once the Turtles are on the elevator platform, Raphael and Donatello have their weapons stuck in their belts; then the scene switches, and the weapons are gone again just before Traximus unpacks them for the Turtles to take.