Continuity mistake: In the exterior front shots of Elliott's house there are some significant changes to the landscape in different shots. For instance, the two lampposts at the bottom of the driveway change to an entirely different style in some shots, and the huge garden boulders repeatedly vanish and reappear. Also, note when Michael takes off on Elliott's bike to go search for ET, the in-ground lamppost that should be beside the mailbox has vanished, but it reappears when all the government agents are setting things up outside the house.
Continuity mistake: When the Jun hoard attack the Emirite village, Dar gets knocked unconscious and his dog starts to drag him away. After Maax arrives, the dog is shown dragging Dar away a second time. Two mistakes are apparent. The dog is pulling on the cloth of his left shoulder in this shot. First, when the dog is pulling, the dog stops to get a better grip on the clothing. When the dog lets go of the clothing, Dar keeps sliding even though the dog isn't pulling. Second, when they show the close-up of Dar, the dog is pulling on his right side, not the left. Then again on his left side and again on his right side. It switches a couple of times.
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.
Plot hole: We learn in the film that Cat People must kill a human in order to return to their human form. However, after becoming a cat at the swimming pool and terrorising Alice, Irena becomes human again without making a kill (the only other person at the closed pool is alive and well at the end of the scene - we know Alice has not imagined the presence of the cat because of her shredded clothes). (01:31:00)