Incorrectly regarded as goofs: The buildings in the city co-mingle architectural styles from three separate Mayan civilizations: Tikal Classic Maya (800 CE), Puuc (c.1050 CE), and El Mirador, a Pre-Classic metropolis that existed around the year 0 CE. This is not an error on the part of the film maker's - it was a conscious decision based upon the desired aesthetic of the movie.
Factual errors: A nearly-full moon is shown the first night after a solar eclipse; this is impossible as solar eclipses only occur during a new moon.
Continuity: 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.
Anachronisms: The Murals in the tunnel are nearly exact replicas of ones dating from 100 BCE - 1,700 years before the movie is supposedly set. The only difference is that the real murals don't show people brandishing bleeding, severed heads.
Continuity: The "sick" girl they meet has her hair covering her right ear, then showing it, covering it again, in subsequent shots.
Crew or equipment visible: When the captives are escorted through the city, there are several close shots at their faces. Shadow of the camera equipment on Jaguar Paw's face is clearly visible during one of the shots.
Continuity: The son of the hooligan leader Zero Wolf gets hurt on the right eye during the attack on the village. His father does two blood pressure release cuts right and below his eye. In the scene where the Commander gives his son the knife, the cuts moved further up and are now on to the right of his eye. And in the "shooting range" scene when the son is "the finisher", the cuts moved even further up and are now to the right and to the top of his eye.
Incorrectly regarded as goofs: When Jaguar Paw jumps from the waterfall and emerges from the water, his wound disappears. This has been fixed on the DVD. Only the blood has washed off; the wound clearly remains.
Continuity: When atop the Mayan sacrificial temple, Blunted's blue paint marks change on his face.
Continuity: The "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.
Anachronisms: In one scene, a bird, a Cattle Egret, is in the scene, but it's an exotic species that wasn't present in the Americas until the 19th century.
Factual errors: The long feathers on the Mayan priests's head dress were those of the Quetzal, a native Central American bird. In the film they are the tail feathers of Reeve's Pheasant Syrmaticus reevesii, a native bird of China and often used in movies when long plumes are needed.
Continuity: Throughout the sequence at the top of the pyramid, the man who Jaguar Paw's group met in the forest at the beginning switches from being at the front of the line to being behind Blunted, and then back to the front again.
Crew or equipment visible: When the character Blunted is being pushed from behind into the hut by his mother in law, you can clearly see a hand pushing against his stomach, holding him steady to give the impression he won't budge an inch.
Crew or equipment visible: Just before the eclipse and the crowd is cheering, it looks like a white middle-aged woman with short gray hair is cheering on the steps with the crowd.
Factual errors: The partial part of a solar eclipse takes about hour and half, while the total part typically lasts few minutes. In this movie however, both parts seem very short and of the same length, and occur in a minute time frame between the sacrifice of the last captive, and an attempt to force the same fate to the main character. This discrepancy then results in a funny effect of the moon seemingly coming to stop during the total phase and resuming its absurdly fast movement after it.
Incorrectly regarded as goofs: At the end of the movie, Spanish ships arrive near Jaguar Paw's village. This is a bit of artistic license, as the classic Mayan civilization (huge temples and mass sacrifice) portrayed in the movie was long gone when Europeans came to the Mayan area of Mexico. Apocalypto really shows Aztec culture at the time of the Spanish conquest, not Mayan. However, the Mayan people still live in southern Mexico and Guatemala, and speak Mayan, not Spanish. They are very much alive today.
Revealing mistakes: When they are making the sacrifice just before the eclipse, at the bottom of the steps viewed from the right hand side shows a pile of torsos and heads. After a couple of frames of body parts bouncing down the steps and being caught in the baskets, a view from the other side is shown, and it is a direct mirror image (reversed film), instead of different bodies.
Factual errors: When the prisoners arrive at the Mayan City, they run into an old man who is said to have laughing sickness. Kuru is a disease of Papua New Guinea (identified in 1900s) and has not been noted in Central America.