Continuity mistake: Watch when Keno puts the pizza box inside the bike's trunk as he bodyshames the unimpressed girls; the tape that seals the box is loose and partially damaged. It's nicely flat and whole when he opens the trunk in front of her home, and with a different shape at its end when he shouts at the robbers raiding the mall. (00:02:15 - 00:02:50)
Continuity mistake: Keno stops his motorbike in front of April O'Neil's address. The passersby don't transition from the first shot to the second. (00:02:45)
Revealing mistake: In the first fight scene of the film, Keno sweep-kicks one of the bad guys. The man falls over without ever being touched. (00:03:05)
Continuity mistake: When the Turtles first arrive on screen behind Keno, they leap over the boy to attack the thieves. Their order from left to right when they walk up is Mikey, Leo, Donny, then Raph. The very next shot shows them in the air, and the order is now Mikey, Donny, Leo, then Raph. Donny and Leo switched places between shots. (00:03:35)
Continuity mistake: Keno strikes a cool pose after downing three opponents at the beginning of the mall scene. As it cuts to a closer angler, the pose obviously changed; his shirt appears poofier and bares a huge part of his black undershirt. (00:03:40)
Continuity mistake: Raphael dunks Keno into the laundry cart. Keno pulls himself up; between the Costume Designer and the Music composer credits 5 seconds pass but during the cut on Raphael kicking butt nearby the sheets he's on top of shifted a lot. (00:04:45)
Revealing mistake: While Donatello is doing the "Ninja Cowboy" gag, in the background Michelangelo slips away from a dogpile and lets the goons beat each other up. It's meant to be a mere background choreography and it shows, since the stuntman on top is "pummeling" the others with the slowest fake punches. (00:05:05)
Continuity mistake: In the sequence with Michelangelo doing tricks with the yo-yo, whenever Donatello is visible in the background he's delivering a spin kick to the same enemy. (00:05:20)
Revealing mistake: During the opening scene a clear divide between head and body of the Turtles suits is particularly obvious in a few sequences, such as when Donatello hogties a baddie and shouts "Ninja Cowboy!" raising his head, or when he plays dummy bouncing left and right. (00:05:20)
Revealing mistake: When Donatello is messing around with the puppet, in the background the stuntmen who are fighting Leo and Mike are doing incredibly sloppy choreographies, or lack thereof, in particular those in the middle (around the doorframe) who literally run on the spot without doing anything. (00:05:45)
Character mistake: When Mike fights by the concession stand at the mall, the Reuben sandwich is misspelled on the menu in "Rueben." (00:06:35)
Continuity mistake: When April arrives at her apartment, she places down a folder like object, and then puts some paper and her keys on them. Next she places her purse on top of the left side of the objects. Moments later, after she goes upstairs, the Turtles come in through the window next to the stuff she sat down. Now the purse is on top of the right side of the items, and the strap is in a different position. (00:08:40 - 00:09:25)
Continuity mistake: When the turtles are watching April interview Prof. Jordon Perry on TV, Leonardo throws the TV Guide, which lands on the table behind Michelangelo with nothing on it. After Raphael complains about Michelangelo chewing the candy bar loudly, he stands up and not only has the TV Guide changed positions, it's now lying on top of another dark object that wasn't there before. (00:16:40 - 00:17:15)
Continuity mistake: Michaelangelo does his "Wax on, wax off" little gag. Notice on the counter two buckets. The metal bucket has no rags in it...except, it does when April arrives and Mike grabs the buckets, dragging that rag back. (00:20:50)
Revealing mistake: In the rooftop scene with Splinter and the canister of Ooze, the blurry fake backdrop is not in the least convincing. (00:21:30)
Plot hole: Splinter knew all along the name of the company who made the Ooze, and literally sat on this vital piece of information for over a decade just because he was too stupid to simply look the name of the company up, written on giant letters and far from being hidden - he merely had to open the yellow pages, no doubt. Nobody with such a telling piece of evidence about their own origins (the canister that mutated them is in his hands and has the logo of the company with the name spelled out) would be unable to find out something this obvious. (00:22:00)
Other mistake: In the TGRI building, the whole computer scene is the kind of nonsense you can expect from something really 90s and childish. Forgetting the fact that Donatello's big fingers are obviously too big to push the keys, the database screen scrolls independently from his movement, and when he tries to "decode" the database, whatever it means, he just types back the serial number. It's all just waving hands around to make it look like you're doing something. (00:25:05)
Other mistake: During their computer hijinks, Leo asks Don "Can you bring up the file?", which the Italian dub mistranslates in a nonsensical "Can you block the file." (00:25:30)
Revealing mistake: When Michaelangelo throws the flask to knock away the canister of ooze, the ooze flies away before the flask reaches it. (00:25:50)
Continuity mistake: The Turtles are looking at the computer in the TGRI lab. The Foot Clan sneaks into the room just as the computer shuts down. Michaelangelo's bandana has both ends behind his head, but they are already in front of his shoulders in the reverse shot before he turns. (00:26:00)
Chosen answer: He had moved away - he says in the third movie. We are never told as to where it was he moved to though.