Audio/visual unsynchronized: When the monks proceed towards the final burning of their prisoners at the stake, they chant. You can see a few monks moving their lips totally unsynchronized.
Miscellaneous: When the monks proceed towards the final burning of their prisoners at the stake, Brother Berangar is among them, though he's supposed to be dead.
Anachronisms: The statue of the Virgin Mary in the church is in Renaissance style but it should have been Romanesque or Gothic.
Revealing mistakes: (At 60:52) When the body of brother Berengar (who was found drowned in the bath) is lying on a table for examination, a shaft of light creeps over the actor's eye, causing him to blink.
Anachronisms: The "Secret Passage Door" is welded with a modern welding technique not used until the late 1800 or early 1900's.
Continuity: When Brother Berangar took the book with Brother William's glasses inside, you can see the traces of the glasses on the pages who was left during a previous shot.
Factual errors: In the trial, Bernardo states that he will take Brother William to Avignon for trial before Pope John. Though it could be considered an Aglicisation of the name, in 1327 when the film was set, the Pope in Avignon was Johannes XXII, not one of the many Johns.