Before April changes her disguise she is wearing a black skirt and full length stockings. She puts a new skirt on over this which is not long enough to cover the black one. She makes no other adjustments to her costume below the waist. Suddenly the first skirt has vanished and her stockings are only knee-high.
In Bebop and Rocksteady's transformation scene, Bebop's boots are shown to be destroyed due to his feet growing with the mutation. However, when he's seen just after the transformation, his boots are fully intact.
When April changes into a school girl's outfit to distract Dr. Stockman's assistant, she grabs a miniskirt and ties it around the skirt that she's already wearing. But we never see her take this particular skirt off. It just magically disappears. She is also wearing pantyhose which suddenly changes to over the knee stockings.
In the parking lot fight scene with Bebop and Rocksteady, Casey finds wheels and duct-tapes them to his boots, planning to use them as Rollerblades. In the following scenes it is obvious and visible that he has full aggressive-sport-type Rollerblades on his feet.
When Bepop and Rocksteady are at the Horseshoe bar talking about climbing up since Shredder is out of the picture, when filming from the right side Rocksteady beer mug is half full. When filming from the left side there is only 1/10 of mug filled.
According to Dr Stockman, Bebop and Rocksteady's new forms are due to dormant genes connected to humanity's animal ancestors. This is partly correct, though clearly not in the way intended: every gene, dormant or otherwise, connects us to our ancestors. But humanity's ancestors do not include rhinoceros or warthogs.
The first day scenes occur on November 1st (the day after the Village Halloween Parade) but all the trees are green and full of leaves. Subsequent day scenes also show summery foliage.
When the turtles are in the hold of a cargo plane they are hot. The hold of a cargo plane at altitude is typically a very cold place.
The M1 Abrams shown in trailer when if fired the round had rifling and is spiraling that means a rifled barrel when The M1 Abrams have smoothbore barrels.
When Vern goes to get recording from a hidden camera in a wall clock, he had to pull out whole wiring from the ceiling/wall and it returns to point just below where actual hidden camera was placed/installed.
An electrician/technician would not waste such a long wire around the hall if had to put the storage device just below it.
The Turtles are afraid of getting shot by the cops in this movie, but in the previous movie, they found out that they were bulletproof when they were shot by the Foot Clan. It is not inconceivable that the Turtles believe the police officers to have different, more effective weaponry than the criminals.
In the first film the shredder is bald and is covered in scars while in this film he has a full set of hair and has much less prominent scarring. However, he survived the climax of the previous film only by exposure to the mutagen's regenerative effects. Apparently that included healing his old scars as well, and even seems to have made him younger.
Pre-mutation Bebop is clean-shaven. As part of the mutation, he grows additional hair out of his ears, near his mouth, along his spine and from the tip of his new tail. All of this new hair is purple, which would only be possible if that were his natural hair colour.
When the jet is in a nose dive, the sound of a prop plane diving can be heard.
The Ducati Streetfighter bikes the foot soldiers are riding have low revving two cylinder V-twin engines. The high pitch sound heard is from a typical, high revving 4-cylinder Japanese sports bike.
When the turtles are shown on a cargo plane returning from Brazil, it is a night scene, but the scenes in New York just before and after the exterior shots of the plane are set in the daytime on the same day, and they arrive back at their lair on that day. The only way it could be light in New York and dark in Brazil is if their plane departed shortly after sunset in Brazil. But by the time they got to New York, the sun would have set there as well, so it should have been night, not day.
The address on April's NYS license doesn't exist. It is so far west on that street that if it did exist it would be about a mile into the Hudson River.
Casey is not believed when he recounts the events from Shredder's escape, however there should be numerous cameras overlooking the roads, including traffic cameras.
The Dodge Challenger driven by Casey has no front plate. This is against New York law. It also seems strange for a corrections officer aspiring to become a cop.