Continuity: When Miguel and Tulio first arrive at El Dorado, the volcano is visible near the palace, but it disappears later in the film.

Continuity: When the two men bump into the skeletons, one of them has a sword sticking out near its head. A few minutes later, Miguel grabs the sword, and now it is much further away from the skeleton's head.

Continuity: When Miguel and Tulio are hiding in the barrels on the ship, they push the corks out so they can breath, but a second later the corks have disappeared from the ground.

Continuity: The shape of the spear that Tzekel-Kan's assistant has, changes in the scene where he first sees Miguel and Tulio next to the waterfall.

Continuity: When Miguel is feeding the birds, they switch position between shots.

Factual error: The real El Dorado (Spanish for "the gilded one") civilization was in South America. The art scheme of the film is Mayan, a Central American civilization, as are the names of the Indian characters. The ball game, too, although not restricted to the Mayas, is, culturally speaking, Central American (and more specifically, and technically, Meso-American). In addition, the Mayan architectural elements found in the movie are typical of the Mayan culture of the Classic Period (c. 250-900 C.E.), roughly 600 years before the arrival of the Spaniards.

Continuity: During the scene when Miguel and Tulio are having an argument, Tzekel-Kan, who is listening to them, changes position between shots.

Continuity: Miguel and Tulio are in a barrel of water when they stowaway onto the ship. So when they burst out of it, why aren't they soaking wet?

Continuity: When Tzekel-Kan introduces the ball-playing team, he states that there are 15 of them. In the next shot, as the team runs back to where they came from, there are suddenly only six of them. The number of players changes constantly throughout the entire ball game.

Continuity: When the people of El Dorado are bowing after Miguel and Tulio 'make' the volcano stop erupting, Tzekel-kan's assistant magically appears in the hallway in front of them.

Continuity: When Tzekel-Kan says "This is how the gods should play ball", the vines, moss, and grass that were covering this arena a few seconds earlier have vanished.

Continuity: Altive kicks Tzekel-Kan's jaguar-like monster in the eye, leaving several cracks, The cracks constantly change between shots, particularly in the scene where the monster has cornered Miguel and Tulio at the edge of the cliff over the water.

Continuity: The skull that Miguel and Tulio meet at the beginning, is very obviously different to the one Cortes crushes later on.

Continuity: When the sailor unrolls the map to show Miguel an Tulio, the stone symbolizing the gods is to the left of the skull. But when Miguel is reading it and says "Look, look" the stone is directly under the skull.