Raka calls Mae Nova, stating that apes name all humans Nova. Nova was the name of the mute human adopted by Maurice in War for the Planet of the Apes. Nova is also the name of Taylor's human mate in the original 1968 Planet of the Apes.

While in the US government bunker, the apes come upon a doll that goes "Mama" in the same voice the doll that Taylor found in the 1968 film which increases the realization that humans once were the dominant species of Earth.

The scene with a scared Mae hiding in the tall grass is shot in the same way as the scene of a scared Taylor hiding from the gorilla hunters in the 1968 film. She even runs up on boulders similar to the way Taylor leapt off a log to avoid the gorillas.

Kingdom of the Planet of the Apes is set 300 years after War for the Planet of the Apes in the Southern California area. Raka's residence is set underneath the ruins of LAX. The clan of Noa reside somewhere within the Los Angeles basin. Proxima Caesar's clan resides near the remains of the Coronado Bay Bridge near San Diego, CA. The observatory is heavily implied to be the Griffith Observatory, based in the Hollywood Hills. This is a nod to the original film saga as the Los Angeles basin is the setting for Escape from the Planet of the Apes, Conquest of the Planet of the Apes, and Battle for the Planet of the Apes. The first films in the "Caesar trilogy" were also set in and around San Francisco and the nearby Muir Woods National Park.

The symbol that appears throughout the movie, such as the one on the necklace that Raka has, is the window design from Caesar's bedroom in Rise of the Planet of the Apes (2011).

Continuity

Near the end of the film when Mae says goodbye to Noa, she is shown to be concealing a revolver behind her back in her right hand. Then Noa offers Caesar's pendant to Mae and she accepts it with both hands extended. The gun has disappeared.



Factual errors

Raka would have needed a larger horse to carry his body weight.

Apes cannot swim, though they have been seen to play in or wade through water. Proximus and his cohorts would likely have drowned when the hangar flooded.

Sylva is using an electric shocker to electrocute Noa, but since Noa is holding an electrical conductor (the electricity tower beam or cable) with both hands, there is no potential difference, much like how birds remain unharmed while perched on high-voltage wires.

An electrical generator, like the one seen in the silo, would not be functioning after "several generations", which is at least over a century if not several centuries. The lights would not function either and it is doubtful any of the computer components would be operable as well due to decay.



Revealing mistakes

The apes climb along the sea cliff, getting completely drenched, yet they are able to light their torches a few minutes later.



Miscellaneous

When Noa is being electrocuted by Sylva while hanging on the metal cable, Noa uncontrollably lets the cable go and falls down. In reality, when under the electronic current, muscles on contrary contract and Noa would not have been able to let the cable go until the electrocution is over and losing his consciousness.



Audio/visual unsynchronized

After the grassland "hunt" sequence, When Raka, on horseback, strikes a chimp with his makeshift club, it makes a distinctly metallic "clang" sound, but the club is wooden; an uprooted small tree and it's root ball.



Plot holes

When the bunker floods, the water is above the level of the ocean and somehow draining from a floor above the apes despite their floor not being flooded.

Eagle tribe is shown using gauntlets made of cloth to protect their hands from the sharp claws. Unless the apes somehow mastered the sewing technique (and learned to grow and harvest cotton), there's no way they'd be able to use gauntlets made over 300 years ago, as they'd tear to shreds almost immediately.

Apes use some sort of uncovered fire lamps in their wooden huts. Naturally, it's a fire hazard, and the entire village would burn down.



Character error

Proximus Caesar tells Noa that he needs 'instant evolution', the implication being that, as humans evolved over a great amount of time from a common ancestor with other apes, it is this fact that allowed them to develop the technology that he craves. However, most of the advanced technology that he is referring to has come about in the last few hundred years, not many thousands, and has nothing to do with evolution, mainly due to the fact that homo sapiens have not evolved at all in the last tens, maybe even hundreds, of thousands of years.

It's doubtful the apes would retain sign language after several generations if they are all capable of spoken language. There's very little use case for sign language, except maybe when hunting in silence.