When the Technodrome is first seen moving at the beginning of the episode, its main eye is colored white.
When Rocksteady is talking to Shredder before they stumble upon the Star of Atlantis, he appears to be gliding across the floor instead of walking.
Some shots of Merdude show him moving around as if he was walking, as opposed to hopping on his tail (he has no legs). He also appears to be hopping ridiculously fast when he and the Turtles try to stop Shredder from escaping the dome.
Rocksteady is in two places at the same time: fighting Michelangelo and Leonardo, and with Shredder stealing the Star of Atlantis.
The cell door that previously held Hepax Lagamina is open when Bebop finds Rocksteady in the adjacent cell, but is suddenly closed after he frees him.
The key that Bebop uses to free Rocksteady from his cell appears to be inserted into the lock backwards.
When Krang aims the Technodrome's eye at Atlantis, the hole in the city's dome and the octopus that was preventing the city from flooding from earlier have vanished. Those dome workers must work fast!
The Turtles are able to breathe underwater in this episode. This is actually a frequent inconsistency throughout the entire series. The Turtles are not sea turtles, as their original real turtle forms had feet and not flippers, which means they shouldn't be able to breathe underwater (and in fact, being reptiles even sea turtles can't breathe underwater and just hold their breaths for up to an hour). Yet in the first episode they are being carried in a fishbowl full of water and clearly having no trouble breathing, and there are numerous times throughout the series when the Turtles are in danger of drowning.