While William and Adso go to the library through the secret passageway at night, the establishing shot outside of the library shows the building in daylight.
When Brother Berangar took the book with Brother William's glasses inside, you can see traces of the glasses on the pages from a previous shot.
After arriving at the monastery, as William peers out the bedroom window before directing Adso to the restroom, he's wearing boots. Moments later when the abbot arrives to greet him, he's wearing sandals.
53 minutes into the film, as the Franciscan delegation approach the abbey, the Aedificium is clearly visible on a mountain summit in the distance. In the same shot a few seconds later, it is missing.
The secret message on the parchment is exposed three times. The translator heated it to reveal the location of the library, William of Baskerville heated it again when he was in the scriptorium and yet again to show the others the message. When a message is written in lemon juice, heating it will cause it to become exposed because the sugar in the juice is caramelized and thus would not disappear again.
Brother William is referred to at least twice as a "monk". As a member of the Order of St Francis (the Franciscans), he was not a monk, but a friar.
Near the beginning, when the abbot comes into the cell where William of Baskerville is alone (Adso having left to seek the necessarium), the abbot greets him with "Pax vobiscum" - but this is the plural form for addressing more than one person. It is taken from the start of each Holy Office, when the abbot would be addressing the choir monks as a group. He should have said "Pax tecum", with William's response being correct as "Et cum spiritu tuo".
At several points in the film, individuals enter another's cell (room) rather freely. In ancient religious rules, entering another monk's cell without permission was normally forbidden, even punishable by excommunication.
The abbot greets Brother Cuthbert of Winchester as "Your Grace". This form of address would only be correct for a high level noble (who would not be a member of an order of poor monks) or in England for a high member of the Catholic Church. It would not be appropriate for a monk in Italy.
(at 1 hour and 55 seconds) 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. This occurs immediately after the close up view of his stained left hand.
As Brother William first enters the abbey he passes a blacksmith beating a piece of obviously cold metal. Such an action would be useless. The metal must be hot to be malleable.
When the dead monk is lifted from the vat of pig's blood and placed on the ground, you can see his closed eyes twitch when they throw water on his face.
When dead Venantius is removed from tank full of blood, Ubertino da Casale quote prophecy of apocalypse. His denture (rotten teeth) failed, because it's moving while he speak.
At 1 hour, 48 minutes and 13 seconds, when brother Jorge de Burgos is speaking in the chapel, the "preservation, I say, not search for" shot shows his right eye a clear. The contact lens to make his eye like a blind man is missing. It is back with the next closeup shot of his face and missing again at the next shot showing his face when he speaks "that the bloody-eyed and cloven-hoofed Antichrist".
The statue of the Virgin Mary in the church is in Renaissance style but it should have been Romanesque or Gothic.
The "Secret Passage Door" is welded with a modern welding technique not used until the late 1800 or early 1900's.
The near-full plate armor worn by the guards for the Inquisition is at least a century too early.
When talking with Salvatore, Brother William seems surprised to find that Salvatore eats the rats he catches. Rats were commonly eaten by the poor in the Middle Ages. Brother William would have been more surprised had someone catching rats not eaten them.
Lemons were rare and expensive in Europe in the 14th century, and it is highly unlikely that a monastery in the mountains in winter would have any, let alone have them available for making invisible ink.
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.
Adso of Melk is a Benedictine novice, not a Franciscan, despite he is called so, together with William.
"Fellow Franciscans.." they're called by Ubertino, for example.
In the book even William addresses him as "you, Benedictines..."
The story takes place in medieval North Italy but most of the characters speak almost all the time modern English. Some Latin is heard, but no local languages such as Italian, German, Rhaeto-Romance languages or Gallo-Italic languages.