During the trial, General Urko picks up a book and mentions the title "the Simian Book of Prophesy", but the book shown is the "Collected Works of William Apespeare", a book which was stolen in an earlier scene.
The missiles on the sides of the barge face the front (bow), but after putting the barge in reverse, the missiles face the back (stern).
When Urko is explaining his plans to detonate the sewers, an Orangotang is standing beside him, with his shoulder positioned in front of Urko. This character should have been positioned behind Urko given his smaller size.
When various apes on the street are expressing their concern of an invasion by the Underdwellers, the characters changes three times but the background remains the same.