Continuity mistake: When Nicodemus is telling Mrs. Brisby that he looked at the words under the latch on the door and understood them, there is a clear, large label under the door. Then a different angle is shown and there is no label on any of the doors, but you should be able to see it still. (00:52:25)
Continuity mistake: Near the start, when Uncle Henry pulls up in the farm wagon in the long shot, the wagon's seat has a high back, but when Aunt Em walks around the horses, the seat's high back is gone, and it reappears when Em sits beside Henry. When they ride away, it briefly disappears, then reappears again.