Other mistake: During the fight scene in the TGRI building, when Michelangelo has the ooze and gets jumped for it and loses it, watch the bottom of the screen. Donatello is lying down and trying to get up. But in the next shot he's up and kicks out the ooze from the foot soldier. (00:26:35)
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)
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)
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)
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: When Keno is trying to join the Foot Clan and is kick boxing with someone, the man in the background who is watching them, to see who is eligible to join, is standing cross-armed. In the next cut his arms are down by his side, and then cross-armed again. (00:43:30)
Revealing mistake: When Raphael and Keno are in the junkyard and the fight breaks out, some of the weapons bend and twist. The staves are supposed to be solid wood. (00:45:50)
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)
Revealing mistake: Tokka tosses Leonard like a bowling ball; the Foot ninjas tumble and fall even when they are miles away from making any contact. (00:53:00)
Revealing mistake: In the junkyard, Leo and Raph grab a long pole and plough through several Foot Ninjas with it. It is painfully obvious the ninjas react to the pole before it ever hits them. Especially the guy on the ground. (00:53:20)
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: 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)
Revealing mistake: There's one scene where they are surrounded by the foot. Leonardo reaches behind him for his katanas, but he doesn't unsheath them. If you look at his elbows, you can see gaps in the pads where the actor in the suit hasn't fully fastened the gloves to the rest of the outfit. (01:05:40)
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)
Revealing mistake: Once Shredder yells "Let the games begin", there is a cut on, so to say, the bleachers with the various Foot clansmember cheering and waving their weapons around enthusiastically. Their enthusiasm is too much and/or the weapons are too fake, because you can see their staves bending and jiggling like toys. (01:06:40)
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)
Revealing mistake: In the part where Rahzar grabs Mikey by the arms and begins swinging him around at the concert, look at Mikey's shoulders. You can see the material of the actor's body suit folding at the shoulders as it is bent further than it was designed for. (01:08:15)
Continuity mistake: The Ooze canisters look completely different from the first movie. The canister in Splinter's flashback was the same shape but had a different label, marked "Radioactive Material" with black and yellow bars. In this movie the canisters had a plain TGRI printed in black. Also Splinter refers to the canister as being broken in half, but in his flashback it is intact.
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.
