Continuity: When Ashitaka swims to Iron Town during the battle, there is a shot of the water. In the next shot there is a floating corpse not visible in the previous shot.
Factual errors: In the movie, Lady Eboshi mentions iron for "Lord Asano and his samurai," however Lord Asano lived 1667-1701 - well after the Tokugawa shogunate seclusion laws that banned firearms.
Continuity: After Ashitaka is shot through the chest, San rides with him on the back of his red deer Yakul, and blood from his wound is seen on Yakul's back. The blood stain disappears after Ashitaka falls to the ground.