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.
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 similiar 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 reside 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.
In terms of the VFX, director Wes Ball was particularly proud of the 33 minutes of full CG (a franchise first) particularly the immense amount of simulated water. The highlight is an action scene with rushing water in a weapons silo. "We flooded a converted parking garage with CG water, and I had the actors put 20 lb sandbags on their legs and walk through the stage so they pretend that like they were in water. That was crazy amount of data. Petabytes and petabytes and petabytes. And we tried very hard to keep a grounded kind of cinema language to it all."
While in the US government bunker, the apes come upon a doll that says "Mama" in the same voice as the doll that Taylor found in the 1968 film. This increases the realization that humans once were the dominant species on Earth.