After stabbing and strangling Priest, Black Hat tosses a lit lantern at Priest's feet starting a fire directly below Priest so he will burn, some of the flames hitting Priest's shoes. However, when Priest later regains consciousness all of the flames are in a semi-circle several feet away from Priest with no burn marks anywhere near his feet.
When Lucy enters the outpost, she passes the mirror and closes the button on her dress. However when she turns back to the table and sits down the button is open again. Then when she stands close to the wall during the attack, the button is closed again.
In many scenes, the cross on Priest's face, which is supposed to be a tattoo, is wiped off from the end of his nose and reappears as a full cross. One of the most noticeable moments in a short time span is at the Nightshade Reservation. Priest has one of the familiars pinned to the ground and when the camera focuses on his face, the end of the cross has been wiped off. Camera switches back to the familiar who points to the sky and when Priest turns to face the sun, the cross is fully drawn on again.
The goof item below may give away important plot points.
At the start of the final battle between Priest and Black Hat, Black Hat kicks Priest into a vent on top of the train car. During subsequent long shots of the train and some shots of the length of the train there are no vents visible anywhere along the top of the train.