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.
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.