Deliberate "mistake": During the gunfire of the Portuguese soldiers at the end, seconds before Jeremy Irons is killed, an old Indian woman is shot in her chest, but the actress/extra forgets to react and continues walking.

Continuity: At the beginning, when Jeremy Irons is climbing the water falls, he is barefoot, but in one shot he uses sandals.

Continuity: In the scene where Robert DeNiro's character renounces his vows of obedience he enters the room with his hair tucked behind his ears. During the conversation with Jeremy Irons's character 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.

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.