When Hob approaches Dalywag (who is tied to the cross) his hand holding the knife is in different positions when viewed from front and rear.
When Osmund is escaping from the ritual performed by Langiva he runs towards water. Running into the water, he is falling down, but not seen getting back up again. In the very next shot, he is seen running again into the same stretch of water.
When Ulrich is saying the Lord's Prayer before the meal at the village, he makes several mistakes in the Latin, including leaving out entirely the last phrase, "But deliver us from evil".
When Ulrich and party come across a group of villagers about to execute a suspected witch in the forest, she is tied to a ladder, which is consistent with witch executions in Germany, where the movie was filmed (the ladder would be tipped backward into a bonfire). In England, where the film is supposed to take place, a suspected witch would be tied to an upright stake and set aflame directly.
Osmund gives absolution (hears confession) from a dying soldier. However, as a novice monk he is unable to do this according to Church rules. Only an ordained priest can.
When the men are tied up in the water prison, Sean Bean's SUFC wrist tattoo is visible. Sheffield United weren't founded until 1889.
The film shows the existence of plague doctors with beak masks, in the monastery. The movie is set in the year 1348, but beak masks (holding smelling herbs or sponges) weren't used until the 1600s.
In the forest the tree stumps have been cut by a modern saw as the stumps shown are flat topped.
When Wolf dies, Ulric's shoe soles show a modern rubber print, not a flat sole that would be more appropriate.
When Osmund is pursuing Langiva into the forest, a large drop of water appears to be hanging in mid air, showing that it is clinging to the lens of the camera being used to film the scene.