Other mistake: The turtles are racing to save April, who is kidnapped by Shredder, and trying to get to the roof. They run into a squad of the royal guards and one of the guards shouts: "Halt! Hands in the air or we'll open fire!" Now, I would like to see that because every one of the guards is holding a sword. (00:14:00)
20,000 Leaks Under the City - S3-E14
Continuity mistake: The Octopus grabs Rocksteady, in the next shot on the boat, Bebop disappears and Rocksteady is on the boat.
Michelangelo's Birthday - S3-E31
Factual error: The very beginning of the episode shows Michelangelo's Birthday circled on the calendar, and it is shown as the second Tuesday of the month as well as being the 13th day. The second Tuesday of a month can never be the 13th. The earliest the 13th of a month can be is the second Thursday.
Suggested correction: This is simply wrong. If a month starts on a Thursday, the first Tuesday will be the 6th, and the second will be the 13th.