When the giant squid grabs Rocksteady from the boat, one shot shows Rocksteady back on the boat with Shredder, when it cuts back to the squid it has Rocksteady in it's tentacle again.
When the Turtles' lair is flooded, Splinter is shown clinging to a pipe. He looses his grip and is shown getting carried away by the water. Before the commercial break he is shown going over a cliff and falling. After the commercial break he is shown still heading towards the cliff and Michelangelo is shown grabbing him and the other turtles before they fall.