In the final showdown with Shredder, Leonardo throws one of his katanas at Shredder, which falls to the ground with Shredder. However, throughout the rest of the scene Leo still has two katanas on his back.
Leonardo's NYC button and the strap it is attached to continuously switches back and forth from left to right throughout the film, sometimes as quickly as a camera angle change.
During the stasis scene three of the turtles are in stasis chambers having their blood removed for the mutagen but there are four tubes filling with blood flowing to the container.
At the end of the movie when Michelangelo accidentally blows up Vern's new car he fires the missile at the rear of the car. The car flips end over end forward, but when it lands the rear end of the car is still facing them. Note the tail lights and open trunk.
During the elevator scene when the Turtles begin to beatbox together, the control panel is lit up for floor 36, then jumps straight to floor 54.
When April is calling Vern to ask for a ride to Sach's mansion, Vern sees April's phone number show on the caller ID before answering. But April is calling from a payphone.
Sacks refers to the turtles as box turtles. Box turtles are a land-dwelling species of turtle. The turtles shown in the film are sliders, which are an aquatic species.
April is Skyping a detective and he asked how she got his number. When you use Skype to call numbers you don't get a video chat. The only she could video chat like that was to call him on Skype and he would have to be on her skype contacts to do that.
When April is doing the fitness interview on the first day of spring in New York City, green trees are visible in the background. Trees in Manhattan do not have full leaf cover until close to May.
At one point, NYPD officers wearing vests saying "SWAT" are shown. The NYPD refers to its tactical team as the Emergency Services Unit. The vests should have read ESU.
Near the beginning when April interviews the fitness trainer and is jumping on the trampoline she is wearing a pink shirt and a black coat. When she walks back to the news van she is wearing a gray shirt with a burgundy coat.
(at around 26 mins) During one of April's video tape reviews one of the turtles' tanks is labeled "Michaelangelo" which is incorrectly spelled. It should be "Michelangelo". This may be explained by the possible lack of knowledge on the part of the very young April.
When Shredder assaults the Turtles hideout where Raphael is leaning over Splinter, the scar on Raphael's lip changes from left to right, as does the hole in his sunglasses changes from right to left lens, indicating that this shot was reversed.
When April is on the docks after the initial attack the turtles make and thwart the foot soldiers - April takes a photo of the "family" insignia on the container with her phone and for a brief moment during the camera angle change you can see that the forward-facing camera is in fact on, thus making it a "selfie".
In one of the scenes with the turtles in the stasis tanks Leonardo is shown in a reverse shot where his shoulder strap is over his left shoulder instead of his right shoulder. Interestingly, though, the animators did digitally reverse the NYC button on the strap so that it was not reversed.
(at around 51 mins) The cameraman's head is briefly visible.
At the beginning of the movie April is doing a story about how to stay fit as it is the first day of Spring yet at the end of the movie the Sachs antenna with the toxin inside falls and destroys the Tines Square New Year's Eve ball and 2014 sign. How can it be the first day of Spring yet the New Year's Eve ball is still on display.
The credits list "Music Preperation" [sic]. The correct spelling is "preparation."
During the introduction, the front page of the NY Daily News is shown, with two sub-headlines. The second reads "City reels after Foot Clan seige." "Seige" should be spelled "siege."
The time-stamp on the footage of the un-mutated turtles in the lab says 1999, which matches the chronology of the film. When we are shown the young April taking this footage in a flashback, she is taking the footage on a bluetooth-enabled digital camcorder, which would not have been available then. The camcorder is also a MicroMV camcorder. MicroMV was not invented until 2001. A MiniDV, Digital8, or even an analog camcorder would have been more period-accurate.
In a flashback, the turtles are watching a music video through a mirror from a sewer vent sometime around 2004-2005 by the CRT TVs in the shop & the song is Hollaback Girl by Gwen Stefani. however, a Nissan NV200 Taxi drives by, the NV200 wouldn't be in production until 2009 let alone a New York City Taxi which went on sale in 2013 for MY2014.
Near the end, when the tower is falling, Raphael gives a speech about being brothers. However, if you look in the background, you can see that the scene is moving in slow motion, but we are hearing Raphael speak at regular speed. In reality is Raphael speaking really quickly?
When April O'Neil calls Vernon Fenwick (who 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.
If the mutagen in the turtles' blood was so precious that the Foot needed to take three turtles, why not take Splinter too? After all, his blood has mutagen in it too, and taking three turtles rather than one suggests every ounce of mutagen is valuable.
April tries to sell the "Vigilante Turtles" story to her boss who doesn't believe a thing and ends up firing April. Minutes later April shows Eric Sacks a photo of the turtles. If she was so interested in getting the story and she already had a photograph, why didn't she showed the photo to her boss?
Consistent with TMNT lore, Splinter and Shredder seem to have an ongoing rivalry with each other. In this incarnation, their epic battle in the sewer is actually the first time they meet each other, thus rendering any history they may have as nonexistent.
When April approaches her editor (Whoopi Goldberg) about the "vigilante story", only to be shot down; it's because April tells her there's "nothing left behind". Despite the fact that April hadn't shown her editor the photo of the Turtles, she had shared the photo of the symbol for "family" and said that the vigilantes had thrown shipping containers at Foot Clan members (which was seen on-camera) -- plenty more than "nothing".
When looking through her father's journals, April sees the Japanese characters for "family" that is noted as the Turtles' calling card. This seems like an unlikely thing to put in a science journal, especially considering that the Turtles learned all they know of Japanese culture from a book Splinter found possibly years after they were put in the sewer.
Consistent with TMNT lore, Raphael holds his sais with two fingers over the "yoku", or curved part of the sai. No one who is even remotely trained in sai-jutsu, or using sais in combat, would hold them in this fashion as it defeats the purpose of the weapon.
When April uses her phone to make a Skype video call to the dock worker (indicated by the Skype logo on the screen) the worker asks April how she got his number. Skype video chat uses screen-names, not phone numbers.
During a flashback scene, young Raphael carves a turtle statue out of a tree stump using his sais. This is highly unlikely since sais are truncheon weapons and are not sharp, but used like batons for bludgeoning.