The ropes binding the last guy to die on the cross in the waves are clearly loose enough to pull your hand out of. Also in one of the later shots the ropes are new, unlike the old dirty ones in the earlier shots.
At 52 mins when standing on the image of Christ - the feet of the prisoners are caked with mud, yet no footprints appear on the slab after they stand on it.
Father Rodrigues meets Monica and he asks her name. Once told, he replies "ahhh, like the mother of (St.) Augustine." He pronounces "Augustine" as "Oww-gus-teen" not the correct "Ahh-gus-tin" in English.
In the scene where Rodrigues and his Translator meet Garupe on the beach, Just after Garupe jumps into the ocean and starts to swim, The Translator is saying dialogue but his lips are not moving for most of the spoken line, and what is spoken does not match his lip movements.