Continuity mistake: When Sarah shouts, "Quick, this way!" and then Sir Didymus shouts, "No, not that way!" the hanging sign with the hammer hangs crookedly by only one chain. However, two shots later when Sir Didymus shouts, "You're going the wrong way!" the sign hangs properly from two chains. Then later, when the three Samurai Goblins jump in front of Sarah and the rest, the sign's chain is broken once again. (01:20:00 - 01:25:40)
Continuity mistake: When Fievel discovers that Warren T. Rat is actually a cat in disguise, the hat tucked into his black belt disappears between shots. (00:51:20)
Continuity mistake: When Grumpy Bear grabs the key on Dark Heart's throne, his left arm changes color from blue to orange between shots. (00:57:25)
Continuity mistake: Just before we see Johnny fall off the bridge we see a shot of him speeding past some roadblocks. Look at the size of Johnny compared to the roadblocks. They are practically bigger then him. This was obviously a small replica robot filmed with the camera on the ground, to give off the impression it was the real thing. (00:20:45)
Continuity mistake: When Carolyn first enters David's room at NASA headquarters, she introduces R.A.L.F. Between shots, David wraps both arms around his knees. (00:30:35)