Factual error: On the left-hand side of Lucy's front door, you can see a blue and white shield. This is the trademark of the Dutch Heritage organisation, which protects monuments such as old city buildings. These signs did not exist in the 19th Century. (00:48:00)
Continuity mistake: When Jonathan returns to his town and don't recognize his wife, his coat disappears in the next shot when he ask to the man beside him who she is. He didn't have the time to remove it. (01:14:15)
Factual error: The Captain of the ship writes in his logs that they travelled the Caspian Sea, the Caspian sea however is land-locked.
Factual error: The carriage brought back the ill Jonathan to Lucy's home in Wisper. But in the road before her door, you can see a modern manhole cover. The film is set in the 19th Century. At that time there was no sewer. (01:13:15)
Factual error: When the ship comes into the harbour of Wismar, you can see the text "Vrijmoed Wittkampf" right above the doors of the warehouses across the harbour. These names are old distillers of the city of Schiedam, proof that the shots are taken in Holland and not in Wismar. (01:06:00)
Plot hole: Supposedly the plague broke out the moment the rats poured into the docks, as well as the plague breaking out when the rats got on the boat. However, these are domesticated rats. Only the fleas on black rats would carry the "Black Death," which is spread by fleas that aren't carried by other rats.
Factual error: The town in which a large part of the movie is shot is supposed to be Wismar, Germany. However the architecture of the town shows it's in The Netherlands. Delft, to be exact.
Suggested correction: Delft was used as a location, but the town square is not all that different from what an early modern North German city would look like. You can spot it if you know the place, but that applies to so many movies. In itself this is not a mistake, unless there were something that really betrayed it.