Goofs

When Taylor looks back at the ship's clock for Earth in Planet of the Apes (1968), it reads November 25, 3978. However, Brent tells his dying commander that the year is 3955.

In both instances, the chronometers were disabled when the ships crashed, stopping at the last known date. In this example, as Brent's ship is far more heavily damaged than Taylor's was, it obviously broke while recording an earlier date.

When Brent and Nova are running along the hillside after the horse is shot, his arm bandage clearly falls off, but in the next shot it's back on again.

As the apes break into the cathedral, Mendez is wearing his purple sash before they enter. After the apes make their way in, it's disappeared.

When Brent first encounters a mutant, Verger, he can see the "alpha omega fins" of the doomsday bomb. He turns and runs back to the double doors, turns around to respond to Verger's "beeps", and in this impossibly short time the bomb has already been lowered into the silo, so only the top is visible.

When Brent and Nova first make their way into the ruins of the subway station, they're both wearing their leather collars from when they were captured. A few scenes later, they're nowhere to be seen.

Taylor gives his dog tags to Nova. In Planet of the Apes (1968), he does not have dog tags when he is captured by the apes, or when he rides off at the end of the film. There is nowhere he would have gotten them since his ship sank and his supplies and clothes were destroyed by the indigenous humans. Even if he had somehow brought his dog tags along, they would have been confiscated by the ape council at his "trial".

Taylor was originally captured wearing the remnants of his uniform, in which he could've placed his dog tags within, having recovered them among their trail of stolen possessions, then Zira finding them sometime later, returning them to Taylor off-camera before they arrived at the seaside cave.

When Brent and Nova come across the first fountain of water with dirty-looking water in the underground ruins, Brent immediately spits it out after trying to drink it. Its dirty and murky appearance should have been a strong indication it was not safe or ideal for drinking.

Brent was also shown trying to drink water dripping from the cave, obviously he was desperately thirsty and hoping that the water in the pool would be somewhat potable despite its appearance.

Although Cornelius and Zira were indicted for heresy in Planet of the Apes (1968), there is no mention of this fact in the film. Since the events of the first film, they have gone from being enemies of Dr. Zaius to trusted colleagues without explanation.

After destroying the cave in the first movie, Zaius may have had a change of heart and pardoned the couple in exchange for the promise of keeping their knowledge of their true history a secret from the ape population.

Just before Taylor disappears in the Forbidden Zone, he tells Nova to "Try to find Zira." Why send her back to Ape City in an attempt to look for Zira? She could risk being recaptured by the apes, or even worse, exterminated. Not to mention they've pretty much become fugitives. Taylor should also know, based on what he went through previously, that this isn't a good idea.

Taylor was confident that if Nova ended up recaptured, Zira would take care of her, which would be preferable to dying in the Forbidden Zone.

When the Apes are faced with visions of fire, a statue of their Lawgiver bleeding, and their eleven missing soldiers being crucified, Dr. Zaius urges Ursus to shoot the suffering captives. Ursus resists, stating that the Lawgiver has forbidden Ape to kill one another. However, later on in the first film, Zaius warned Cornelius and Zira they could hang for high treason.

Ursus was hesitant to shoot "innocent" apes, even if it was intended for humane reasons. This is different from apes being executed for committing serious crimes.

In the "steam room" scene, Zaius and Ursus are wearing only towels, yet they seem to have twice as much body mass naked than when they are wearing their clothing.

Obvious pull-over ape masks on many of the apes in the background during Ursus's speech to the Ape Council.

During Ursus's speech to the Ape Council, James Gregory is very animated. He is so animated, in fact, that near the end of the speech he turns and lifts his head, revealing his throat and Adam's apple.

When Brent finds the pay telephone in the subway he hits the stone wall and it gives, revealing it is only foam.

At the beginning of the film where Brent meets Nova for the first time, two taped position markings can clearly be seen on the ground behind Brent. These markers appear and disappear between shots.

The underground telepathic mutants claim to be a "peaceful people" but the idea of "get[ting] [their] enemies to kill each other" as well as inflicting deterrents on who they consider enemies contradicts such a statement.

When Taylor and Nova are riding through the lightning, in one shot there are tire marks on the right side of the frame.

When Brent tries to get the reins from the runaway horses you can see an extra set of reins going into the paddy wagon through the holes in the wall, to a hidden driver. After Brent stops and dismounts, the reins disappear.

When Brent fights the gorilla on top of the jail transport cart, the gorilla stands on his neck, but is knocked off the cart by a tree branch. He then lands on some hay. The cable pulling him backwards and onto the hay is visible.

As Brent and Nova start to ride away from the wrecked spaceship, a white paper cup blows from the camera position. It blows along the ground into the center of the frame and then around behind the horse.

Brent was sent on a rescue mission to look for Taylor and his crew. There was no need to send Brent on a rescue or recovery mission as it would have taken place decades or centuries later than would have been possible or necessary.

When Dr. Zaius is visiting Cornelius and Zira, he refers to them as "You two psychologists". Cornelius is an archaeologist, not a psychologist.