Corrected entry: The main background villain in the story is Hernando Cortez, but he didn't come to South America to seek El Dorado. He subdued the Aztec empire in today's Mexico between 1519 and 1521. The only Spanish expedition to seek out El Dorado at that time was under the command of Gonzalo Pizarro.
Corrected entry: When Tulio is bashing his head against the wall of the ship, the sounds that are heard don't match him hitting his head.
Correction: I checked this scene a couple of times and I didn't see anything wrong.
Corrected entry: Throughout the film, the characters keep using the phrase "to err is human, to forgive . . ." (not usually finishing it). The thing is that the movie is set somewhere around the year 1500 (right after the introduction song, they show you the year when the story is supposed to take place) and that phrase was "made famous" by Alexander Pope, an English poet born in 1688.
Correction: If it was only "made famous" by Pope, then it may have pre-existed him, perhaps even back in 1500.
Corrected entry: The movie is set in 1495, and the main enemy is the historical leader Hernan Cortez. Cortez was born in about 1485; he should be about ten years old.
Correction: The movie isn't set in 1495, it's set in 1519 as it says in the beginning, so that would make Cortez about 34, which looks very much true to the animated character in the movie.
Corrected entry: After yellow-hair has eavesdropped on black hair, he sadly walks down the steps. Altivo (the horse) walks down after him. HORSES CAN'T WALK DOWN STAIRS.
Correction: Actually, horses can walk down stairs, it's cows that can not.
Corrected entry: 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.
Correction: Because it's meant to take place in a different arena.
Corrected entry: When Tulio puts the dice into his vest, he puts them into the right side. When he's scooping up the gold and the dice fall out, they fall out of the left side.
Corrected entry: When the armadillo is used as a ball, it frequently defies gravity.
Correction: This is a cartoon, and as such, they don't follow the normal rules of gravity and physics.
Correction: It is never stated that Cortez is searching for El Dorado. As he says, he is searching for "Gold, glory, and Spain". It is Miguel and Tulio who search for, and find El Dorado. Since Cortez never actually "finds" El Dorado (because the entrance is destroyed), there's no historical mistake here.