Twice, the sloth's head is initially at the man's right shoulder, then on the left in the next cut.
When Gabriel slips on the rocks near the beginning, climbing shoes are briefly visible before he climbs barefoot again.
When Mendoza comes to ask Gabriel for his blessing, Gabriel is sitting at the desk writing. Gabriel puts away his quill and turns toward Mendoza. In the next shot, Gabriel turns towards the desk, still writing, and says "No." In the following shot, he looks directly at Mendoza and is not writing.
During the attack by the Portuguese, Father Gabriel's monstrance changes between shots.
The woman painting the right side of Rodrigo's chest completes an arc to his upper abdomen. After a cut, she is just starting the painting on his upper right chest.
The movie uses the Spanish honorific "Don" as a translation of the English "Lord" or "Mister", and Cabeza is repeatedly addressed as "Don Cabeza". "Cabeza" is a surname, and "Don" is used only before a first name. The correct Spanish equivalent would be "Señor Cabeza".
On a few occasions, the Portuguese currency is referred to as "escudo". At that time, Portugal's currency was named "real". "Escudo" was only adopted in 1911, one year after the advent of the Republic in the country.
Near the end, when Father Gabriel marches with the Indigenous as the Portuguese are shooting, one elderly indigenous woman in front of Father Gabriel is shot. Blood bursts onto her white loin cloth. She keeps marching, suggesting that she missed her cue.
The indigenous characters speak Wawnana, a Colombian indigenous language, not Guarani, the indigenous language of Paraguay.
When Cardinal Altamirano visits the missions, the cut glass decanter is a Regency or Victorian style produced after the early 1800s.
In the opening credits, when Liam Nesson points to the falls, the platform tourists walk on when visiting the Iguazu falls is clearly visible on the left side. The platform was built in 1940, the film is set in the 1750s.
The Chief Minister of Portugal during the time period the film takes place (before 1758) is referenced twice as Marquis of Pombal. However, the title was given to him only in 1769.
While Father Gabriel is playing an oboe at the waterfall, his fingers don't move in sync with the tune.
After the Guarani boy sings, Cabeza calls him an animal. Father Gabriel gives a speech in the boy's defense. During the crowd's reaction, a brief cut to Father Gabriel shows his lips not moving, even though he's still speaking.
All Portuguese and Spaniards speak English all the time instead of Portuguese and Spanish.