Mistakes

During the final battle against Shredder, Leonardo accidentally drops his katana sword from a building with Shredder.  For the rest of the scene, he has both katanas on his back shell.

Leonardo's belt button switches from left to right a lot through out the movie and as fast as a camera angle switch.

In the mountainside lab, three of the Turtles are having their blood removed into four tubes to a container.

At the end of the movie, Michelangelo accidentally blows up Vernon's car by firing a missile at the car rear.  The car flips end over end forward, but when it lands the rear end of the car is still facing them.

While the Turtles are riding the elevator up, the controls light jumps up from floor 36 straight to 54.  

April wears a black shirt on the top of the building, but when she goes to the sewer, she's wearing a gray shirt.

Michelangelo's rocket skateboard appears and disappears between shots, but it's strange, because he didn't have the skateboard with him when he went to the mountain top earlier.

When April is biking to the docks, it is clearly night when she is on the bridge, when the attempted robbery is taking place, and when she is talking to Taylor. She even mentions it to her roommate: "it was night." But in the transition to the newsroom, it is still only dusk.

When April gets fired from her job, after the first day of spring (see her fluff piece in the beginning about how to stay fit in springtime), Vern drives her to Sacks' mansion. When they arrive, there is snow on the ground and it appears to be mid-winter. Yet they didn't pack or fly, so it is driving distance from New York City, where it is purportedly springtime.

When April and Vernon are at Eric Sacks compound lab, Foot soldiers fire shots at the van, cracking a window, but then when the van crashes into a door and reverses, the window is undamaged.