Continuity: When Miguel and Tulio are lost at sea in the rowboat, a seagull lands on one of the oars and then dies. They try to get it, but a shark gets to it before them, and bites off the oar while doing so. In the following scenes, the oar is intact again.

Continuity: When Cortes comes to the El Dorado island, he sees that Miguel and Tulio's footprints lead directly from the boat to the jungle. But this is not what happened. Miguel and Tulio arrived to the island, bumped into two skeletons, ran back to the boat, walked around the beach for a while, and THEN went into the jungle. This is what the footprints should have shown.

Continuity: When the two men are under the deck planning an escape, Tulio has a black eye. A little later, when they are escaping by boat, the black eye is gone. A black eye would have taken longer to heal.

Continuity: When Miguel and Tulio jump out of their rowboat yelling "It's land." you can tell there's nothing on the beach. But then they kiss the sand and a skeleton has appeared.

Continuity: As Miguel kisses the sand he bumps into a skeleton. The skull is the first part he sees. However when the camera rises over the skeletons, you can see the skeleton's arm is stretched out. It wasn't there earlier.

Continuity: When Miguel and Tulio first arrive to the island, they bump into a skeleton. When Cortes arrives at the island later in the film, there's only a skull. The bones that were there earlier have vanished.

Continuity: At the start of the ball game Tzekel-Kan puts the ball down on a flat surface, shouting "Play ball.' But in the next shot there are a couple of tiny pieces of rock near the ball.

Continuity: When Miguel kisses the skull after arriving at El Dorado's island it is facing towards the ocean. But when Cortes arrives later on, it is facing away from the ocean.

Continuity: When Miguel and Tulio first arrive at the El Dorado island, the moss and plants near Whistling Rock (shaped as an eagle's head) change between shots and also change later in the film.

Continuity: When the monster corners the two men at the edge of the cliff, there are no vines on the ground. Then after punching Tzekel-Kan, Tulio says "Tie him up" and vines have appeared.

Continuity: At the start of the film, when Miguel wins the map, he rolls it up vertically. Later in the film, when they first arrive at the El Dorado island, he takes it out of his shirt and unfolds it horizontally.

Continuity: After Tulio and Miguel arrive in El Dorado, Miguel's earrings disappear and reappear between shots.

Continuity: When Miguel and Tulio first enter the city there are plenty of vines at the entrance. But when they sail out of it at the end, there are no vines.

Continuity: When Tzekel-Kan puts the ball on the floor shouting "Play ball," the shadow of the ball is at a completely different angle than it is in the next shot of it.

Continuity: At the end, Miguel notices that Tulio's sail is stuck, so he rides his horse down a huge staircase and jumps onboard in order to save him. In the shot of him jumping on the horse for the first time, the natives are seen in the background on the same level, holding onto their ropes. Then Miguel starts riding down the staircase, and suddenly they are all the way at the bottom, by the river.

Other: In the scene where Tzekel-Kan reveals the big tiger thing, he is on his knees facing it. He says "do as I command" and raises his right arm and the tiger raises his left arm. The tiger and Tzekel-Kan should both raise the same hand because the tiger is built to mimic Tzekel-Kan's exact moves.

Continuity: After Tulio tells the sailors that they have nothing to bet with one of them replies "Oh yeah, I got this" and shows them the map. When he does this, the face of the weeping woman on the map faces to the left, however later in the film when the two men use the map to identify where they are, the woman's face faces forward.

Continuity: When Miguel and Tulio are sailing out of El Dorado and almost hit a stalactite, between shots the stalactite becomes more pointy.

Continuity: After Tulio successfully rolls a seven and wins the map, the dice are visible near the large pile of gold. Then as Tulio begins scooping it up, the pile is much smaller, and the dice are not there anymore.

Continuity: When Miguel and Tulio see the fountain shaped as a weeping woman, there are plenty of trees nearby and rocks are visible in the middle of the river. Later in the film, when Tzekel Kan surfaces at this area after falling into the whirlpool, the nearby trees are totally different, and the rocks in the river have vanished.