When Roy starts telling his first story about the soldier bringing a helmet with the last of their water to Alexander the Great, the soldier is clearly seen to be galloping on his horse without the helmet, but it magically appears as he dismounts.
When Alexandria is making shadows on the wall with her fingers while waiting outside Roy's door, she is using her right hand when we see her hand from inside Roy's room, but in the next shot, in the hallway, she is using her left hand.
When Governor Odious sends Charles Darwin the dead Americana Exotica butterfly, it's an iridescent blue color with no markings. When Wallace chases after and catches a live one, Darwin looks it over and claims this one is the Americana Exotica, even though this butterfly is orange with black and white markings, not shimmery blue like the first one.
When Alexandria brings Roy the communion wafer she takes a big bite leaving nothing but a sliver left but in the next shot she offers the rest to Ron and it is much bigger than it was when she took a bite.
Though the hospital scenes take place in Los Angeles, they actually shot in South Africa, which drives on the left side of the road. All the cars in the shots on location at the hospital have steering wheels on the right side of the car, revealing that they are not actually in LA.
As Otta Benga is carrying Alexandria away from where Governor Odious' men are killing the Mystic, there is an overhead shot in which the viewer can clearly see Odious' men purposefully missing the Mystic with their kicks and stomps, so as not to injure the actor.