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 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, it proves that the Spirit only walks on the water surface.
The goof item below may give away important plot points.
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.