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 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 Chihiro is sitting at Zeniba's table, there is a large slice of cake in front of her during close-ups, but no such slice is visible during long shots.
The smudge on Chihiro's face changes shape, switches sides, and disappears at random during the first 40 minutes of the movie.
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 Haku says "Even the tiniest breath will break the spell, and then everyone will see you," his lips aren't moving at all.