Visible crew/equipment: Thin wires are visible, attached to the crystal bats as they fly off to watch Jen and Kira.
Continuity mistake: The sequence in which Dragon is chasing Mrs. Brisby through the field, up the tree and eventually into the mill's lake, watch his eyes. The original placement is (from viewer's perspective) blue on the right and gold on the left. When he chases her up the tree the gold one is visible on the right, it then switches back when the camera cuts back to a wide shot. This happens again a few seconds later near the lake.
Revealing mistake: When the bugs crawl out of E.G. Marshall's mouth, it is obviously a dummy.
Continuity mistake: At the start, when Aunt Em and Dorothy exit the house, Em holds a basket on her arm, but in the close-up, the basket has vanished as Em adjusts her hat. In the next shot, the basket reappears.
Continuity mistake: In the scene just before the snowman comes to life, the clock in the hallway reads midnight. But a little later, when he is showing the snowman around the house and he is about to lead him upstairs, the clock reads 8:05.