Plot hole: While it is essential to the story, there is a problem with apes in the space ship. While it is the one that took Taylor to the future, there is no way the chimps could have salvaged the ship from the water (plus there wasn't enough time for such a salvage operation. Kira and Cornelius were living in the ape city we see in "Beneath the Planet of the Apes" never mentioning to Brent that they found a spaceship he could travel back with). They didn't have the technology for such an operation, no diving suits, and chimps are scared of water. Also, the water would have destroyed the power systems of the ship when it sank. (00:00:25)
Revealing mistake: Throughout the film, when the camera goes close to Zira, you can see the line where her wig is glued on.
Revealing mistake: At the end of the film as the camera zooms in on Milo as he's starting to speak, the part where he says "mama" is on a loop. (01:32:35)
Other mistake: As the opening credits roll, the helicopter that brought officials in is taking off. Trouble is, the sand is rushing in back under the chopper rather than blowing away from the rotor wash.
Other mistake: When Cornelius and Zira should escape through the mechanical door that is opened by a knob in the guard's box there is no way that Cornelius could see which knob he should press, because one of the guards has his face turned to the window that they are hiding under.
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 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: 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 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)
Factual error: Zira puts the blocks together to form the stairs that will allow her to get the banana, but only stares at it. When the female scientist asks why she won't eat it, Zira says she loathes bananas. Bananas grow in tropical climates near the equator. New York City, where she lived in the future, is in a subtropical climate zone, and not grown there. How would she loathe bananas if she's never eaten one before?
Suggested correction: There is too much we don't know and too many possibilities to declare this a mistake. Perhaps they have trade with lands further to the south. Perhaps the climate has changed and land around New York is now hospitable to bananas. Perhaps in the two thousand years between our time and hers, a strain of bananas developed that thrives in temperate environments.
Revealing mistake: On the boat, just as Zira says "We've met hundreds since we've been here and I trust three", you can just make out the actress' real teeth behind Zira's fake prosthetic teeth and ape make-up. (01:24:35)
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)