As Zach gets away with the emerald, Don Turtelli grabs Caitlin. In one shot when Turtelli is making a deal with Zach, Zach is shown where Caitlin is being held by Turtelli.
When Don Turtelli opens up the grate over the secret opening in the floor of the basement, the grate is flat on the floor when it's opened but when he's about to depart, the grate is standing up while it's open.
When Donatello puts Caitlin on his back, there are crates behind them when Caitlin says that she knows where the computer room is. Then the next shot of them, there's a painting on the wall and no crates.
The Rat King's hair frequently changes from lighter orange to darker orange during certain shots.
After the rat attack and the museum is locked up. When one of the police officers is pulling on one of the doors and falls over, the handle is missing as he was pulling on the door.
When Raphael says "I look terrible in stripes" his mouth doesn't move.
During a closeup of Zachs feet as he is being tickled, in the background Caitlyn appears to have two left feet.