Continuity mistake: When Elliott gets food for himself and ET he takes the milk container from the top shelf of the fridge, and we see an empty space beside the Skippy peanut butter where the milk had been, but after Elliott drops everything onto the floor, in his next two closeups note the milk container (it has a distinctive curved design) is back on the shelf in the same spot beside the Skippy jar.
Revealing mistake: Every time Dar's village is from the hill, it is a blatant scale model or matte painting where all the people and animals are suddenly missing.
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: In the training simulator at the beginning of the film, after Sulu and McCoy have both fallen, McCoy has his head resting on Sulu's hip at first. Then, in the next shot, his head is resting closer to Sulu's knee. (00:05:50)
Revealing mistake: When Conan is fighting in the ring and smashes a guy's body against some [prop] rocks, the painting cracks and falls off.
Revealing mistake: When Alan gets up to go to see Dillinger, look at the cubicles. The first row that Alan came out of is real. In the immediate next row, the cubicle that is adjacent to Alan's has no visible exit, and the two that would be heading toward the white wall seem to be only leading to each other. The rest of the cubicles in the area are all a matte painting used to extend the set.