Revealing mistake: When McDonald is in the tunnels and is called to pick up the phone, he picks up a red phone. It is a standard Bell TouchTone desk phone. To make the phone look more futuristic, there was no cord and it was disguised as a cordless phone. The port that the cord would plug into is covered by a piece of colored tape. This also can be seen in the operations center of Ape Control when the worker picks up the phone.
Revealing mistake: In the electrocution scene, whenever Caesar is screaming you can see the hole in the roof of his mouth for Roddy to breath through the front of the makeup.
Revealing mistake: During Caesar's big speech at the end, you can tell in some of the close-ups of his face that his mouth isn't moving.
Chosen answer: Caesar wasn't the only surviving ape, just the only surviving talking ape. Conquest of the Planet of the Apes is set roughly 20 years after Escape from the Planet of the Apes, and in that time man began to keep apes as pets (disease wiped out dogs and cats) and (most likely through breeding), the apes evolved into what we see in the film.
Bishop73