Conspiracy - S1-E25
Continuity mistake: In the beginning of this episode, Riker orders Geordi (who was navigator at the time) to increase to Warp 6. In response, Geordi replies, "Aye sir, full impulse."
The Catwoman from Channel Six - S2-E12
Continuity mistake: When Leonardo cuts off April's collar, she asks what happened, but instead of it being Leonardo standing there with the sword, it's Donatello with the sword.
Continuity mistake: When the Wooly What's-it releases the rock blocking the cave to Rainbow falls, the water splashes on the fobs. When they hop over and jump in, one of the fobs disappears and reappears.