Continuity mistake: When the scientists are using the blocks on Zira, Zira is told to point to the blue blocks. As she points, the blue block is at the front of the pile from the scientist's perspective. In the next shot, the blue block is suddenly in the middle of pile. (00:13:30)
Continuity mistake: The scientists tell Zira to put the shaped blocks back in the box. She starts by placing an orange heptagon in the box, followed by a purple square and blue square, followed by a blue triangle. This is all she puts in the box in this shot, but by the next shot, a red star has appeared and an orange shape has appeared in the corner of the box. Also, the blue square has vanished and Zira then puts a purple box down in its place. (00:14:10)
Continuity mistake: When the guard with the milk and the oranges enters Cornelius and Zira's cell, the jug is 60-70% full. As the guard says "You better drink your soup and eat the oranges...", there is less milk in it. (01:01:35)
Continuity mistake: After Cornelius knocks out the guard with the food tray, he makes for the door. He places his right hand on the door next to the wall, but as he exits the room in the next shot, his hand is suddenly wrapped around the door frame. (01:01:55)
Continuity mistake: When Doctor Branton drives up to the facility, the guard says to her "You lost, miss?" During this shot, Branton's driving hand is placed on the left hand corner of the wheel. Next shot, the hand is placed on top of the wheel. (01:07:50)