Continuity mistake: When the apes are breaking into the command post, just as Breck says "Shoot them! Shoot them all!", the door is about half sliced down. A few shots later, the door is almost entirely sliced down with no time to do so. (01:13:25)
Continuity mistake: After the apes began revolting in the communication center, Governor Breck shoots an ape in the face. Blood splatters on the uniform of the officer holding the ape. A moment later the officer stands up, but his uniform is clean. This is the unrated version. (01:36:30)
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