Toward the end of the movie when Ford is chasing Captain Bergman, in one scene, the night skies are clear except for some distant clouds (visible because this night sky was filmed during daylight hours using a filter to darken the scene so that it appeared to be "night"). Then an actual night sky is shown full of clouds and lightning flashes. In a moment, and very suddenly, the sky goes from being clear to dark and stormy.
At Mitla, Colby shows Julie a hole, indicating that it was a place for offerings to the gods, including human sacrifices. In central America, cenotes (or sinkholes) were used by the native population as water sources and also were used for offerings of human sacrifices and objects. However there are no cenotes at Mitla.