In one of the episodes (the one where April turned into a cat) there were two huge slip-ups.

First, when Leonardo contacts Irma via the Turtles' videophone, she sees Raphael on the screen, who still says that he's Leonardo.

Then, when the hypnotized April come to the sewer to kill Splinter, Leonardo pulls his sword out and jumps to April but when he's completed his jump he turns into a Donatello, who still holds Leo's sword.