Continuity mistake: 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 mistake: When the two men are running away from the soldiers, they see two water barrels and there is no board underneath them. A second later, the men jump into them, and now there is a board underneath them.
Continuity mistake: The number of natives holding onto the ropes to prevent the giant statue from falling keeps changing in the final scene. There are usually several huge rows of them, but in some shots there are no more than 15 or so.
Continuity mistake: When the two men are climbing over the fence to get away from the bull, you can see that the the part of the fence they're climbing is made up of 15 planks, but in the very next shot it's made up of 9 planks.
Continuity mistake: During the song "On the Trail We Blaze" Miguel and Tulio pass by a rock shaped as an animal with its mouth open and there are vines hanging over it. Later in the film, Tzekel-Kan leads Cortes and his men to this rock, and the vines hanging over it are different. (00:19:05 - 01:13:30)