Factual error: After the sewer invasion, April watches the three captured turtles drive away, then she turns to go to Splinter. Shortly thereafter, the computer screen shows GPS tracking the turtles at a location easily over an hour away from Manhattan. Likewise, the estate is referred to as being just forty minutes away from the city. (00:56:10 - 00:58:50)
Continuity mistake: When Leonardo, April, and Vern are hanging from the cliff after the semi truck falls off. April's arm is dangling beside her. The next shot from above, she is hanging on to Leonardo and then her arm drops beside her to dangle. (01:15:10)
Plot hole: When April O'Neil calls Vernon Fenwick (drives the channel 6 van), he answers his phone and immediately says "O'Neil". When the scene cuts back to O'Neil, we see she called from a payphone. Fenwick would have no way to know it was her calling.
Factual error: In 1999 when April is filming inside the research facility, you can see her video camera displaying Bluetooth, which wasn't available in cameras until 2002.
Plot hole: On the night after April meets the turtles for the first time, she has her boss come to her apartment and tries desperately to try and convince her that the turtles are real, unfortunately her boss wasn't convinced and she ends up getting fired. However, April had already taken two pictures of the turtles on her phone the night previously (before meeting the turtles and after they had left the roof and began jumping over other roof tops). She could have easily just shown the pictures to her boss and she would have been convinced the turtles were real. Even if Donatello deleted the picture she had taken before meeting the turtles, April had still taken a picture of the turtles after they left the roof and jumped from other roof tops, so she still could have easily been able to prove they exist.
Revealing mistake: When April O'Neil first tries to take pictures of the foot clan activity at the docks, almost every time they show her phone, the screen is black. In fact, when she finally tries to get the shot of the Vigilante we see a clear as day reflection of herself on the screen.
Revealing mistake: At the end of the movie, the Turtles accidentally destroy Vernon's new car. If you look closely at one of the last shots of the movie where you can see the car now upside down, you can see the car doesn't have an engine, presumably to make it easier to flip.
Plot hole: The turtles are taken away to have their blood drained for the mutagen but Splinter is left behind. How come Splinter wasn't taken? He also has the mutagen in his blood.
Suggested correction: Because April told Sacks that she saved the turtles she never said anything about Splinter being saved as well. So Sacks assumed that only the turtles survived and Splinter didn't.
Other mistake: At the beginning of the film when April sees the foot clan braking into the shipping container, it is pouring with rain, yet her hair miraculously remains dry all the way through.
Continuity mistake: Halfway through the film, when the turtles ask April to meet them on the rooftop, she is wearing a plain black top under her yellow jacket. In the next scene when the turtles have taken her to their lair, she is now wearing a light grey shirt with a symbol on it.
Other mistake: When Donatello is deactivating the countdown, the last 5 seconds on the countdown is shown and the voice on the computer is heard counting down each second. Every one second the voice on the computer counts down is actually two seconds passing in real time.
Continuity mistake: In the scene where the turtles are in the elevator singing MC Mikey, visible to the right of shot is the elevator's control panel and a light lights up every time they pass each floor. Just as the shot ends, the light lights up for floor 34. In the next shot, the elevator stops at floor 54.
Continuity mistake: There is a scar/cut above Raph's top lip. Through out the movie, it is constantly switching sides of his mouth.
Continuity mistake: In the scene where Raphael, April and Vernon are breaking into Eric Sacks' mansion with the Channel 6 van, the guards begin firing at the van and in one shot the windscreen is fired at and it shatters. A few seconds later, the windscreen is suddenly intact and the damage is reduced to just a few bullet holes.
Other mistake: When the turtles blood is being drained, all four tubes have blood running through them, even though there are only three turtles in the containment boxes.
Other mistake: When April views the tapes of her dad she's around 10-11 in them, but Sachs looks the same as he does in the film and this took place in the past perhaps 15 years, before current times.
Continuity mistake: When April goes to the rooftop for the first time, the ladder is a normal ladder that abruptly ends. When it cuts to her taking the photo, it is a ladder that curves over and connects to the roof, then when she is brought away from it, it briefly goes back to a typical ladder.
Continuity mistake: As the semi stops on the mountain, the camera pulls back to show the down slope, and it has trees and rocks all over. But after the truck starts sliding down and turns around, it now has a clear path to slide through.
Continuity mistake: As April increases the injection of adrenaline, the counter goes fro zero to maximum twice between shots.
Continuity mistake: When the turtles return April to the roof after erasing the pictures off her phone, she takes more pictures holding her phone horizontally. Then, at Eric Sachs manor when she shows him the pictures, they are shown to have been taken in vertical mode.
Suggested correction: That isn't a plot hole. Vernon assumed April was the person calling him and was correct. People do this all the time in real life.
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