Other mistake: As Taylor realises what man did in the years from his leaving until his return, he is slamming his fist on the dirt screaming "Damn you all to hell." In the first Apes movie, he didn't give this final line until he was amid the surf waters, but here the water was a couple feet from him.
Audio problem: When Zira and Cornelius return home discussing stuff, Zira begins making chocolate icing. As she makes the icing, she says "Gorillas are cruel because they're stupid." When she says "stupid", her lips never purse together on the "p" but that doesn't stop her from being able to say "stupid." (00:24:15)
Continuity mistake: In the sauna, when the general says twelve of his finest scouts vanished and Zaius corrects him by telling him it was eleven, there are visible steam clouds around them. The general then stands up, and the steam cloud around them has suddenly vanished. Some steam is still visible, but the steam around the two has definitely vanished. (00:22:25)
Continuity mistake: In a flashback sequence of Taylor and Nova, Taylor is trying to get Nova to say her name. In the shot where he is gesturing the word "Nova" with his lips and repeating the name, the end of this shot shows a strand of hair flying over Nova's face and her hair is blowing backwards. In the next shot, the hair strand is gone and her hair is blowing forwards. (00:11:30)
Continuity mistake: As Nova approaches the wreckage of the ship, Brent is shown hiding and holding the shovel in his hand. In the wide angle, the shovel is held almost up to Brent's chin, but in the sudden close-up of Brent, the shovel is suddenly lowered with no time to do so. (00:09:55)