When Leonardo picks up a slice of the marshmallow and pepperoni pizza to offer to Splinter, the marshmallows are not shown on the slice when Leonardo picks it up. In the next shot, there are marshmallows on it.
After April puts the princess costume on, the yellow dress she had is on the chair near the window. After Shredder and his goons kidnap her, the dress is gone.
April's turtle com gets stepped on by the emperor. When he picks it up, it's flipped on the opposite side from the way it was when April dropped it.
The turtle's positions change around between shots when they encounter the guards after the emperor's announcement is made on the loudspeaker.
The embassy is about 3 stories high, but the floor dial over the elevators display 7 floors.
During the closing credits, director Reg Lodge's first name is spelled as "Red" instead of "Reg."