After the woman is killed by the piranha fish, the blood disappears when the river is viewed from the land.
When Mathews and another convict overturn a wagon full of rocks on their pursuers, the position of the wagon changes after the cutback.
When the pirates first arrive at the Huguenot fortified village, they survey the area from the high hills surrounding the village (0:36:06). However, when two of the pirates and Jonathon Standing start walking down the path toward the village, we notice the imposing hills surrounding the village have become mere cliffs, just a few feet high from the ground (0:36:09). Also, the cliffs are located much closer to the fortified village than the imposing high hills from the previous shot.
When escaping to the swamp, Jonathan is shot in the back, yet after left for dead and continuing to escape further into the swamp, he has no wounds on his back, but his left shoulder appears to be wounded on the front side.
When the blindfolded pirates fight and a pirate hides inside a wooden frame, he is shown in subsequent scenes with his sword, either straight out in front, or to the side against the frame.
Piranha fish do not behave as depicted (instantly approaching and quickly devouring any large creatures which enter water near them). That is a myth.
The 'golden' statue is clearly made of wood, the size and weight of it would have crushed the wagon, would have been impossible to pick up without a heavy block & tackle pulley system, and it easily rocks in the wagon when jostled, as well as when the tree fell and knocked it off the wagon.
During the blindfold fight, the blindfolds appear to be thin gauze that the pirates can see through. At one point, when the pirate hides inside the wooden frame, he glances down at a railing before he places his hand on it.
When one of the pirates stomps with his foot at the bottom of the pit they're digging, the sound it makes is clearly that of hollow wood, yet he says that they have reached the bottom and there is nothing but rock (1:03:17).