(at around 1h 40 mins) When Jaguar Paw is in the trees and sees the torch lights of the hunting party, the close up shows his labret (lip) piercing missing. When he turns around, the piercing is back again.
During the attack on the village, Zero Wolf's son gets hurt on the right eye. His father does two blood pressure release cuts below and to the right of his eye. When Zero Wolf gives his son the knife, the cuts moved further up to the right of his eye. During the "shooting range" scene, when the son is "the finisher", the cuts moved to the right and the top of his eye.
(at around 58 mins) Sick Girl's facial wounds change color and shape. At one point, when she is staring forward, the wounds are inverted, most notably the one on her chin.
On top of the Mayan sacrificial temple, the blue paint marks on Blunted's face change.
When Seven stitches Turtles Run's leg using ants as staples, she soothes his discomfort by telling him she just requires one last ant. However, there's is still about an inch of open wound left when said ant is applied.
We see a solar eclipse and that night the moon is in the sky. Given that the (new) moon was on the Sun-ward (daytime) side of the Earth and given that it takes 28 days to complete a full orbit of the Earth, the (full) moon could not have been in the night time sky within 24 hours.
(at around 1h 55 mins) The diameter of the tube created with the leaf to shoot the blow-darts was far too large to propel a dart without feathers or cotton to block off the escaping force of breath. A dart alone would barely make it out of a tube of that size, as most of the breath would be wasted blowing right over the top of the dart.
A solar eclipse can only take place at new moon. However, the night following the eclipse has a full moon.
There are piles of hundreds of corpses dead less than a month, just outside the city, and more piles of hundreds of freshly killed corpses inside the city itself. At no point in the life of the Maya, and definitely not in the 16th century when the film is set, would the surrounding jungle have been able to provide a population large enough to yield that many sacrifice victims.
There was no total solar eclipse in Mexico or Central America in 1502.
(at around 1h 45 mins) When Jaguar Paw jumps from the waterfall and emerges from the water, his wound disappears. This has been fixed on the DVD; the blood has washed off, but the wound clearly remains.
(at around 58 mins) As the captives approach the Mayan city, they come across a girl and her dead mother. Both of them show clear signs of smallpox, particularly the blisters on their face. However, smallpox is a disease brought to the New World by the Europeans and, since the film takes place before the arrival of the Spanish, it's impossible for them to have contacted the smallpox virus. However, this is suppose to be an obvious foreshadowing because the little girl reveals to the captives that a man who comes bearing the Jaguar was going to kill them in the future. She wouldn't know about this unless she was from the future.
During the sacrifice just before the eclipse, a pile of torsos and heads is just right of the bottom of the steps. After a few frames of body parts bouncing down the steps and being caught in the baskets, a view of the other side shows a direct mirror image, not a different pile of bodies.
The seam of Seven's artificial belly can be seen when Jaguar Paw greets her and his unborn child for the first time.
When Zero Wolf applies the first incision to Cut Rock's swollen eye, the prosthetic material is clearly visible as such in the very first shot.
(at around 2h 5 mins) At the end of the movie, all three characters are staring in the same direction. As the camera zooms in to Jaguar Paw, the character behind him on the right is clearly following the camera. Four seconds later he's looking straight into camera on his right. Watch the whites of his eyes.
The style of sacrifice portrayed in this movie are Aztec in style e.g. taking out peoples hearts and throwing the bodies down the temple, in the Mayan culture at this time they would sacrifice through decapitation.
(at around 1h 9 mins) The murals in the tunnel are nearly exact replicas of murals dating from 100 BCE, 1,700 years before the movie is set. However, the real murals don't show people brandishing bleeding, severed heads.
The frog used to create the poison darts is clearly too large for a "poison dart" frog, which are nowhere near the size of American bullfrogs, which this one appeared to be with yellow tree frog colors.
(at around 48 mins) At the beginning of the scene where one of the (wounded) captives belonging to Jaguar Paw's tribe is thrown into the canyon, a Western Cattle Egret (Bubulcus ibis) can briefly be seen. Although naturally spreading throughout the Americas in the previous century (presumably from stragglers flying in from Africa) the first record of the Western Cattle Egret is from the Guianas in 1877. The species established permanently in the 1930's in that area. After spreading north, it established in Mayan country somewhere between the late 50's and early 60's.
(at around 1h 20 mins) When the crowd cheers just before the eclipse, a white middle-aged woman with short gray hair is cheering on the steps with the crowd.
When Jaguar Paw runs through foliage to escape the Holkanes, the tracking camera moves some leaves in front of him.
When the captives are escorted through the city, several close-up shots show their faces. In one shot, the camera equipment casts a clear shadow on Jaguar Paw's face.
(at around 15 mins) When Blunted's mother-in-law pushes him into the hut from behind, a hand is clearly pushing against his stomach, holding him steady to give the impression he won't budge an inch.
Jaguar Paw and the enemy chasers arrive at the beach in heavy rain, with an overcast sky. Bright light reflects off one enemy's shoulder.
(at around 1h 13 mins) The long feathers on the Mayan priest's headdress are supposed to be Quetzal, a native Central American bird and endangered species. They are actually the tail feathers of Reeve's Pheasant (Syrmaticus reevesii), a native of China.