Continuity mistake: When Tiger and Fievel are doing their musical piece, Tiger wipes off the mirror and they appear the same size. When he lays out in front of the mirror, singing the line "We'll be there to pick each other off the floor", he places his head next to the cage bottom, still laying on the floor between them. In the mirror, however, that cage bottom is not reflected at all.
Continuity mistake: Just before Gussie leaves Mickey O'Hare's wake, Fievel can be seen in the background behind Honest John eating a large piece of cheese from a nearby teacup. However in the next shot he's standing in a completely different location and no longer has any cheese in his hands.
Continuity mistake: Watch the small bed inside the water tower. Soon after the song 'Somewhere Out There', a small piece of cloth appears from nowhere on it.
Continuity mistake: When Warren takes Fievel to his henchman Moe who is a rat, he is the same size as Moe. He is even able to go through the very small hole in the wall into the room. Later in the movie, Warren is now seen being the same size as a cat.
Continuity mistake: After the Giant Mouse of Minsk lands in the ocean, a vacant pier can be seen from an underwater perspective. But once the angle changes seconds later, all of the mice are suddenly looking down below at the wreckage. Additionally, two ropes appear from nowhere hanging over the pier's edge.
Continuity mistake: During the storm, Fievel crawls to the edge of the step he's on and watches two fish flop around below deck. Keep an eye on his blue hat. At first it's in his left hand, but between shots the hat somehow jumps below the step he's on - from which he pulls it out with his right hand and places it back on his head.