"Who Wants to Have Eternal Joy" was filmed at two different times. If you watch for it you can see the lighting, as well as the hair length of Phegis Rilbin, change back and forth.
Director Jonathan Decker has a cameo, as described in the film itself, because actor Merek Davis had to go home early. Rather than pretend it hadn't happened, Decker decided to make a joke of it and address it directly.
Characters repeatedly state "Book of Mormons" to pluralize what should be "Books of Mormon."
The master version of this film was on a VHS tape that got crumpled for a few seconds at the beginning. Even on the DVD and online digital version there is evidence of this during the opening credits.
When Indy, lying face down, is hit in the back with a chair, you can see the rock behind him that the chair actually hit.
Actor Jonathan Rogers wasn't comfortable riding a four-wheeler at the speed required by the film, so he was replaced with other actors who wore the hat and jacket. If you look, you can see his pants change color from khaki to black to blue and back to khaki as a result.
To create the four-wheeler chase rudimentary green screens were used in the director's backyard, with numerous revealing mistakes including color changes depending on what the actors were wearing, shadows on the backdrop, and shadows of the camera operator on the actors themselves.
The clipboard stolen from the crew and used as a prop in fight scene does not have the scene or take written on it, as the director forgot to bring chalk.
In several shots, starting when Indy first enters the cave, the cord of the camera can be seen drifting in front of the camera lens in the top right corner.
When Short Round has the duct tape ripped off of his face, actor Brett Hall hesitates before delivering his line. That's because he was recovering from the very real pain of having duct tape ripped off of his face.