Dragon's bad eye switches from his right to his left throughout.
The string Mrs. Brisby uses to lower herself down from the birdcage changes position in relation to the cage bars.
When Mrs. Brisby is caring for Timothy, there is one low-angle shot where the bed appears empty - you can see most of the pillow, but Timothy's head is not on it.
Mr. Ages's cast is on his left leg, but when seen through Nicodemus' "crystal ball" the cast is on the right leg (flopped shot).
The first shot of the Brisby home after the move shows no one outside. A couple of shots later, Mrs. Brisby and the children are outside. When Jeremy appears on the following shot, there is no one outside again.
The Great Owl is heard flapping his wings when he leaves his tree. Being nocturnal hunters, owls' wings are silent as their feathers greatly reduce the noise caused by turbulence.
When Mrs Brisby thanks Jeremy for saving the medicine, she wipes her eye; at this moment, her left and right eyes move slightly out of sync (her left eye's movement downward is slightly delayed).
When the characters enter the lantern elevator/submarine, the initial establishing shot depicts a panel on one side of the lantern pivoted open in order to act as a door, and blue glass is visible within its frame. However, in the next shot, the metal frame of this open panel is incompletely drawn, and does not hold any blue glass. Instead, the whole empty doorway side of the lantern has a blue tint, so that when Mrs Brisby enters the lantern, she appears to walk through a solid pane of glass.
Both the tractor that almost plowed into the Brisby house and its driver are obviously flickering, poorly photocopied live action footage that distracts from the main animation.
When Dragon leaps at Mrs. Brisby when she is climbing the tree, his left claw is shown covered by the base of a tree limb.
Timmy's siblings made no effort to save him, nor could he save himself, Yet somehow he survived being dragged under the mud.