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: 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)