Minor Plot hole: The ninja turtles are huge 8 feet tall green monsters – and yet they fit effortlessly in the sewers and man-holes.
Minor Plot hole: When April is calling this other dude who has a crush on her in order to hitch a ride – he sees her phone number show on caller ID even if April is calling from a payphone.
Major Plot hole: April gets a picture of the 4 ninja turtles jumping off a building. In the next scene, she tries to persuade her boss of their existence and she doesn't show THAT picture and instead astutely decides to show a 15 year old video of her and the normal-looking turtles when they are in their cages. That’s great thinking April; you won’t look crazy at all! Oh wait – you decide to show the good picture to the bad guy right after being fired for not having any good proof to back your crazy story? God damn.
Major Plot hole: Why did Shredder and his merry-men of useless stuntmen extras want to beat the shit-out of Splinter instead of capturing him? He is full of mutagen blood like the other turtles and yet they leave him to die in the sewers – seems a little retardedly contrived.
Major Plot hole: How can Splinter know about Shredder? He wasn’t a scientist in the lab when Splinter was just a rat in a cage – and it’s not like Splinter ever left the sewers after hiding there to take care of the turtles. So when did he develop this antagonism towards this cyborg-samurai he never met?
Major Plot hole: So Shredder fights Raphael one-on-one; defeats him and then quickly leaves the scene without addressing the more important problem of April O’Neil and this other dude trying to free the 3 ninja turtles upstairs. What? Why was it so important for Shredder to leave as quickly as possible? They made their plan sound like they had to release the deadly gas as soon as possible but nothing would change if they took an extra 5 minutes to look at the turtles getting drained of all their blood instead of leaving them almost unattended. They didn’t have to rush their plan – the time-frame was a lie!
Super Plot hole: The rich bad guy’s plan is to get richer by spreading a deadly virus on New York City and by being the only supplier of the cure. That’s already suspicious in itself but the fact that he planned to start spraying the gas from the top of his fucking tower means he would be arrested by federal agents right after forensics, camera footage and testimonies would pinpoint the origin of the gas to his property (which would be around 24 hours tops). So his plan makes no sense; good luck with the sequel guys – we’re optimistic about the franchise.
Plot contrivance: April O’Neil’s father, a scientific genius and piss-poor pyromaniac, starts putting his lab on fire and dies in the process (because whatever) while his daughter makes the most logical decision ever: put her life in jeopardy to save 4 turtles and a rat while looking at her father slowly melting into a horrific flesh monster that would hunt her dreams for the rest of her life (except it doesn’t).
Plot contrivance: Splinter becomes one of the best ninjas in the World by reading a children picture-book about ninjas. That’s it. No training with anyone – no video tutorial of anything – just simple pictures in a book.
Plot contrivance: The Ninja Turtles are bullet-proof except when tension needs to rise in certain fight scenes like this one in the sewers where the foot clan shoots them with tranquilizer darts.
Unaddressed Issue: If April O’neal’s father wanted to destroy all of Project Renaissance by burning the whole lab – why did he leave a metric ton of research papers in his house? Was he planning to burn them afterwards? And since he failed to do that– why didn’t the bad guys show-up to his house to see if any research was left there?
Unaddressed Issue: What was the plan of escape of the villains after they release the deadly gas on New York City? Did they all inject themselves with the cure already? Remember that they were in a super-important hurry to get to that building as fast as possible – so it is rather unlikely that they synthesized enough cure for every men, let alone inject it.
Unaddressed Issue: With all the CCTV cameras in New York City – it seems impossible to fathom the possibility that none of these huge giant monster turtles with colorful headbands would never be caught on camera. Especially considering the fact that they take the time to leave their unique graffiti everywhere they go.