Be Bop wears a hat when moving the Neutra-Freeze from the S&K Warehouse during Operation Ice Station, but in several close up shots he is not wearing the hat; it appears back on his head in the next wide shot.
When Michelangelo slips whilst skating on the ice in the sewer, his nunchuks are in his belt, but when he spins around in the next shot they have disappeared.
When Shredder is talking to Krang with the video communicator, on Krang's screen Shredder is seen holding the communicator which would be impossible since it's what he's being videoed from. The communicator also changes color from purple to gray and back.