Continuity mistake: When Robert DeNiro renounces his vows of obedience, he enters the room with his hair tucked behind his ears. During the conversation with Jeremy Irons, the camera cuts away and returns showing that DeNiro's hair has changed style - the camera then cuts away a couple of times and when it returns his hair is behind his ears again. (01:25:00 - 01:26:00)
Factual error: In the San Carlos Mission are visible Matarraton trees (Gliricidia sepium). They only grows in the tropics of America (Colombia, Venezuela, Panama), not in Paraguay or its borders with Argentina and Brazil.
Factual error: The cardinal mentions the Marquis of Pombal. Sebastião Mele would be the first to receive that title, but that would be 20 years after the film is set. Mele received the title of Marquis in 1770, a full 15 years after the Cardinal's visit.