These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: All of the Mayan warriors are a particularly nasty lot, but none stand out so much as the vicious Dragon to the lead hunter Zero Wolf Middle-Eye. One of their best hunters and fighters, Middle-Eye is also the only rapist, who takes one of the women of a conquered village into a hut to violate her, and kills her after, as her husband Blunt struggles futilely to save her. When The Hero Jaguar Paw nearly kills Middle-Eye in a fight, Middle-Eye vengefully slits his father's throat in front of him and names Jaguar Paw 'Almost' in response. When the new captives are being marched back to the capital city, Middle-Eye at one point decides to lighten the load by throwing an exhausted slave to his death. Middle-eye stands above his fellow slave hunters in depravity and the others consider him sick.
Moral Event Horizon: Zero Wolf, Middle Eye and the other slavers collectively cross the horizon during the attack on the village and the grueling march to the Mayan city. The one that takes the cake must be Middle Eye gloating and killing Flint Sky in front of his son Jaguar Paw, simply for the crime of being Jaguar Paw's father (and for stopping Middle Eye's rape of a girl earlier on).
The refugees are kind of creepy when they appear. Then Jaguar Paw has his eerie prophetic dream which features one of the refugees standing before him, beating heart still in hand, eyes bulging widely, panting desperately, his heart beating faster and faster until it's thundering loudly. Then he manages to gasp out one word: "Run!"
The raid sequence, which features children being slaughtered and women raped.
The scene of the decaying Mayan civilisation and the desperate people thereof.
Unfortunate Implications: The film has been very polarizing in their portrayal of the Mayan people and the arrival of the Roman Catholic conquistadors in the film's ending, which can easily be seen to be saying it was a karmic punishment for the Mayans.
The Woobie: Blunt, being the object of cruel pranks and mockery from his fellow villagers while being constantly insulted by his wife's mother for being unable to have children. Then, when the Holcanes arrive, Blunt bravely fights back but gets overpowered...and has to watch his wife being raped and killed in front of him by Middle Eye.
It becomes a Tear Jerker when Blunt and the other men are marched off to be sacrificed, and his wife's mother touches his face as if to comfort him...and his later Heroic Sacrifice to give Jaguar Paw a chance to escape.