After Tulio and Miguel arrive in El Dorado Miguel's earrings disappear and reappear between shots.
When Miguel and Tulio are looking down from the roof, they see four barrels. After they jump, there are many barrels. When the net picks them up, there are six barrels.
When Tulio and Miguel are stranded, the shark bites off the end of the rudder. In the next scene, it's intact again.
When Tulio and Miguel are "arguing" about throwing off Tzekel-Kan, Tzekel-Kan changes position in the background between shots.
When Miguel wins the map, it is rolled up vertically. At the treasure hunt, it's rolled up horizontally.
Cortés didn't sail from Spain in 1519, but from Cuba, where he had been living for more than a decade.
In real life, Hernan Cortes was a rogue captain who disobeyed orders from Diego de Cuellar, governor of Cuba, and was off to conquer Tenochtitlan, the capital of the Aztec Empire. The most famous explorers that did try to find El Dorado were Francisco de Orellana (who actually disappeared in the Amazon looking for it) and Lope de Aguirre, later immortalized in Werner Herzog's "Aguirre the Wrath of God" (1972)
All of the Spaniards - Cortez, Tulio, and Miguel - immediately speak the same language as the inhabitants of El Dorado, when in fact the natives would not have known Spanish.
(at around 49 mins) When zooming on Miguel, who he is supposed to be swinging around the pole hanging upside down, no pole is seen in the background.
Tzekel-Khan's hand passes through Cheif Tannabak's torso when the former asks for Miguel and Tulio's preferred proposal.
When Tzekel-Khan proposes a ceremony for the evening, he refers to then as dawn, when the term should be dusk.
When Tzekel-Khan proposes a ceremony for the evening he refers to it as dawn, when it is actually called dusk.
The main characters make mention of the peseta as a currency. The peseta wasn't introduced until 1869, exactly 350 years after the time the movie is set in.
Cortez stated that once they touch land, Tulio and Miguel would be sent to Cuba to work as slaves on sugar cane fields. The cultivation of sugar cane in Cuba began in the 18th century. In the 16th century, the name of Cuba was "Isla Juana".
Altivo's apple can be seeing bouncing off a telescope on Cortez's ship. The telescope was not invented until the early 1600s in the Netherlands.
The movie is set in 16th century Spain, but when Miguel and Tulio are about to jump into the barrels they bet 2 pesetas on it. Pesetas weren't in circulation until the 19th century.
When Tulio is bashing his head against the wall of the ship, the sounds that are heard don't match him hitting his head.
Considering at least a few days should separate Tulio and Miguel's arrival on the island and that of Cortes, their footprints shouldn't have still been there for him to follow.
Tulio mentions how they are now richer than the King of Spain. In 1519, there was no title 'King of Spain' The man who ruled Spain, Charles V, was known as the Holy Roman Emperor and ruled Spain as King of Aragon, Castile and Léon. The title 'King of Spain' was not used until Charles' son, Philip, became king in 1556.