Corrected entry: The scene at the graveyard takes place at Nazca, but after the scene, when the route they fly is marked on the map, they fly out of Cuzco. Cuzco is far up in the Andes, and it is very unlikely that they'd travel by land that far and then fly from Cuzco.
Correction: They would have to if that was the only place they could fly out of. This isn't a mistake.