When San receives the crystal dagger necklace from Ashitaka she ties it on and it is visibly separate from her wolf tooth necklace. A few moments later when she climbs onto the back of one of the wolves, the crystal dagger is part of the wolf teeth necklace and is not on a separate cord. Later in the movie the two necklaces are separate again.
While Eboshi and Jigo are speaking to each other in Irontown, Captain Gonza is seen standing directly behind Eboshi. The next scene shows a close-up of Jigo. The scene after that pans back to Eboshi and shows Gonza has been replaced with a man in a hat.
When Ashitaka spots San for the first time at the river spitting out a mouthful of Moro no Kimi's blood from the bullet wound in her chest, the number of large wolf teeth on San's necklace changes from four, to three, back to four.
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.
Throughout the movie characters refer to their weapons as "rifles" and call those using them riflemen. However none of these weapons are actually rifled as can be seen in various shots. The first version of the weapon is more accurately defined as a hand cannon, the version created by the lepers is a primitive smooth-bore.
When Ashitaka first visits the Forest Spirits home, he spots the Spirit's traces (shape of his hooves) underneath the water surface. But later in the movie, the spirit is seen as a walking surface, which is regarded as a goof. It isn't. The spirit, shishigami, can do whatever it pleases.