When Haku has collapsed and turned back into his original form in the boiler room, he is seen clearly lying down with his head facing Kamaji's post. Then when Sen says her goodbyes to him for now, he is no longer pointing to Kamaji's Post. He is seen back facing his post when he wakes up.
The smudge on Chihiro's face changes shape, switches sides, and disappears at random during the first 40 minutes of the movie.
When Haku shows Chihiro how to get to Kamaji the door to the boiler room opens inwards and when she eventually comes there it opens outwards.
When Kamajii bangs the wheel to alert the Mushi-balls, a chopstick clearly falls down from the bowls. However, when he is cleaning off the dust only a minute later, there are two chopsticks again.
When Sen and Lin are asked to clean the "big tub" before they start to clean it the tub appears full with dirty water but a few seconds later Lin and sen are stood in the tub but it is empty.
When Yubaba flies back to the Aburaya with the bag, she clearly flies above the side of the deck. However, in the next shot, the bag hits the side of the deck.
After Haku flies out of the bedroom we see Sen's left hand touching more of the blood on the railing. The elevator attendant sees it on the same hand after grabbing her arm as she tries to board it. Not much later we see her looking at the same hand again before running across the pipe. It isn't till after being held captive by the baby under the cushions that the blood switches hands as he holds her by the left arm revealing no blood on that hand at all.
When Sen steps in the Black Slug in the boiler room, the slug goes all over the bottom of her foot. When she kneels down next to Haku, the black slug remains are no longer on her foot.