When the humans from the dead city and two of Aldo's gorillas meet in the desert, Governor Kolp watches the gorillas through his binoculars. He then issues orders to shoot the gorillas with a cannon. The cannon fires in a completely different direction to the way he was looking, but hits them anyway.
When Aldo returns on horseback after the big battle, Caesar is seen standing very close next to Virgil in a close-up. In the next shot, Caesar is still walking towards Virgil.
While in the destroyed city, Virgil states that the radiation level is 300 roentgens. At that intensity, it would have killed Kolp and his people long before the events of this film.
Like too many films with battle scenes, mortars and grenades are shown doing explosive damage only. The purpose of such weapons is not to damage by explosives, but the explosive charge to disperse shrapnel fragments used to maim and kill.
A fall from that height would not kill a chimpanzee or a gorilla.
When teacher Abe speaks the word "No" to General Aldo, he is told that this is a banned word and no human is allowed to say this word to an ape ever again. Minutes later, in Caesar's hut, Caesar asks MacDonald whether his parents are still alive and he answers "No". There is no negative reaction from Caesar because he knows MacDonald is simply answering a question, not giving an order.
Caesar's famous "Now, fight like apes!" line is marred by his ape lower-mouth appliance beginning to fall off, revealing his own human mouth inside. The director tried to hide this by blurring those frames of film at the lower end of the screen. What looks like dust on the camera was intentional.
When Caesar and his search party pause on summit of a sand dune and first see the Forbidden City in the distance, a place where no one supposedly visits, we see them continue their approach on a well traveled sandy path full of fresh footprints ahead of them.
When the governor opens the silo doors it is obvious that they are barely big enough to let the main body of the missile through, but not big enough to let the fins out as well.
During the final battle, several of the explosions are really the same single pyrotechnics gag (a blast that destroys a tree house and splits the tree in two) shown to us from different angles.
When the apes escape the ruined city, sand dunes can be seen on the horizon - a line can be seen running down the sand dune background, revealing it to be a matte painting.
When McDonald plays clips of Zira and Cornelius speaking, there is sound, but the images are video stills. There is no reason for such files to be edited to use a video still with sound, so the method that the clips are stored with is an oddity.
During the final battle scene, a pyrotechnic charge and the cable leading to it are clearly visible at the bottom of the screen (at around 14 mins). The holes in which other pyrotechnics charges are buried are visible before they explode.