Continuity: When Gabriel slips on the rocks near the beginning, climbing shoes are briefly visible before we once again see Gabriel climbing barefoot.
Factual errors: Indian characters don't speak Guarani - the language of the Paraguayan Indians - but Wawnana - the language of the Colombian Indians who performed in the movie.
Audio/visual unsynchronized: In the scene in which the young Guarani boy sings heavenly, but Cabeza calls him an animal nonetheless, Father Gabriel gives a speech in the boy's defense. The gathering's reaction is first observed, but as the image briefly cuts to Gabriel, it is visible that his lips do not move, even though he is not through with his speech yet.
Continuity: The sloth's head is initially at the man's right shoulder, but then on the left in the next cut. This happens twice.
Continuity: During the attack of the mission by the Portuguese, the monstrance held by Father Gabriel is different between shots.