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: 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: 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)
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: 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)
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: The broken donut looks different in Rahzar's palm from the close-up to the moment before the fight begins. (01:08:10)
Continuity mistake: In the first phase of the final showdown with the monsters, Shredder calls them to battle shouting "Tokka! Rahzar! Let the games begin." Midway through his shout-out there's a cut, and the Ooze canister is tilted differently. (01:06:30)
Continuity mistake: Once Chief Sterns has delivered his off-the-record speech about his off-the-record record, April chases him around to actually get something off him; in the background you can easily tell by the sudden shift in sunlight on the store signs and tents that time has passed between the two shots. (01:00:30)
Plot hole: Shredder unleashes Tokka and Rahzar in a residential part of New York. The time is not stated but two senior citizens are taking a cab and there are a cafe and other stores open, it's not quite the middle of the night. Yet the police and the journalists are on the case only the morning after in full daylight. (00:59:45)
Continuity mistake: When Raphael is captured, the Foot soldiers hold him in front of Tatsu, and then Shredder. The side of his head receives direct sunlight or not depending on the camera angle. (00:46:50)
Plot hole: Throughout the movie, the strength of the two beasts fluctuates heavily; they can chew and break telephone posts with ease, they can toss a Turtle many meters in the air through a roof, but they are caged by makeshift cells of junk poorly pieced together or a little horse trailer. (00:39:30)
Continuity mistake: April runs inside her office to get the call. Her boss angrily says "She's busy with her news manager" etc.; to the right side of the screen, notice a man in a pale blue shirt and beige pants. April in the next shot picks up the receiver and says "Donny?"; in the background, that extra is only now walking to the desk he was previously standing in front of. (00:38:15)
Factual error: In the scene inside Channel 3's open space, there are several wall clocks, but they are wrong. When it's 10:05 in New York it's not 3:05 in Frankfurt, London and Paris; besides, 3 clocks out of 6 which always point the same time is really wasteful - not that London is in the same timezone as the other two, but here they all point at the same time. (00:37:25)
Other mistake: The Italian version of the movie keeps the "All the good ones end in -O!" joke that singles Raphael out, making him angry and causing his punishment...but the Italian names of the Turtles ALL end in O, "Raffaello" included. (00:31:05)
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)
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)
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)
Plot hole: The timeline of the movie is quite strange; April obviously got her job back and made advancements in career, living in a sweet two-floor loft. At least -some - time must have passed, many pizza deliveries and all that, but Shredder just woke up from the pile of garbage he ended in at the end of the last movie and the Foot hasn't attempted any reaction or organization yet, implying it is set mere hours after the first movie.
Plot hole: It's never really addressed or explained how Shredder survived his death in the previous movie from being crushed in a garbage truck.
Suggested correction: It didn't really need to be addressed, and thus is not a mistake. His hand emerging from the junkyard is enough to show that he survived his apparent demise at the end of the last film.
