Revealing mistakes: Wires can be seen coming out of Leonardo's shell at the beginning when they are all eating pizza with April.
Revealing mistakes: In the junkyard scene, part of Marc Caso's arm can be seen when Leonardo reaches for his katana blades and his costume opens up at the elbow.
Miscellaneous: When Keno is running from The Foot's Soldiers in the junkyard aka. The Foot's HQ, you see him fighting against two of The Foots soldiers, and another guy running in the back, ready to do jump over the junk in front of him, and do a saltomortale. Before the saltomortale, he jumps up into the air, like he is about to jump onto a trampoline.
Crew or equipment visible: During the fight in the TGRI lab with the Foot you can clearly see a mat in the background as one of the Foot Ninja lands in the background.
Continuity: During the junkyard scene, just before Donatello is thrown, you can clearly see that Leonardo's katanas are in their sheaths. After he is thrown the shot cuts back to Leonardo fighting and his katanas are no longer there.
Audio/visual unsynchronized: At about the 52:47 mark after Donatello is thrown through the roof and rips the tape off of the TGRI guys mouth he exclaims "I gotta get the hang of that" to which the TGRI guy says "That's okay." immediately after "That's okay" you can hear someone on the set say "Teenage Mutant Ninja Turtles 107" in the background. Use headphones if you must.
Revealing mistakes: In the first fight scene, Keno does a sweep on one of the bad guys, Keno clearly misses but he still falls to the floor.
Audio/visual unsynchronized: At about 37:58 when Shredder tells Tatsu to remove the bar because "it's time they learned who their master is", the shot goes back to show Tatsu from the front, where his lips are clearly moving, but there is no sound.