Audio problem: When the Christian army is defeated after chasing Saladin across the desert, many vultures are flying over the battlefield. However, the sound is that of a flock of whooping cranes.
Audio problem: In the scene where the guys held down Troy to burn him with the USMC symbol, and he's crying on the floor, you see Jake Gyllenhaal's character move in and you can hear him whisper, "You earned it, man," but if you read his lips, he is actually mouthing "Asshole!" (01:17:05)