Continuity mistake: When April changes into a school girl's outfit to distract Dr. Stockman's assistant, she grabs a miniskirt and ties it around the skirt that she's already wearing. But we never see her take this particular skirt off. It just magically disappears. She is also wearing pantyhose which suddenly changes to over the knee stockings.
Factual error: During the ceremony on Liberty Island at the end of the movie, Chief Vincent wears three stars on the lapel of her dress blouse. In actuality, an NYPD chief would wear stars on her shoulder plate.
Continuity mistake: When April is running with the canister, she has it in her right hand. The part where she has to put her hands on the car, you see it go from her right hand immediately to her left hand in the next shot.
Continuity mistake: When the Foot Clan attacks the prison transport, Jones looks into the side-view mirror to see a motorcycle following them. The convoy SUVs trailing the prison truck are not seen, just in that one shot. (00:16:55)
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.
Continuity mistake: When we first see the Technodrome building itself and Donnie is analysing it on his computer, we see a number on the screen slowly counting upwards. In one shot the number is in the 331,000 range. A few shots later, it passes by this number again.
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)
