Continuity mistake: The head and eyes of Krang's robot body change entirely after his scene with Shredder early in the movie to a different look later when he fights the Turtles.
Continuity mistake: After the outbreak Bebop and Rocksteady are talking at the bar and the level of beer in Rock's glass changes between shots.
Character mistake: When April and Casey are in the interrogation room April says she wants her phone call. The detective says the phones are down and April reply's with "well hate to break it to you, legally I'm entitled to a phone call." The detective should know that this is not true at all. They can make a call if the detective is OK with it, but it is not a right. (01:04:25)
