Continuity mistake: When Dr. Frankenstein introduces himself to the monster with a soothing "Hello, there", his right hand is on the restraint over the monster's chest. The next shot shows the doctor placing his hand on the restraint again.
Factual error: In the scene right after pinback shoots the beach-ball alien, we see the Dark Star space craft cruising past a planet with a sun in the background. You can see a reflection on the planet which is coming from the space craft. I'm sorry, but usually ships in space are not large enough to reflect off a planet, especially to the degree this one does. (00:48:20)
Visible crew/equipment: In the scene in which Zed & his fellow exterminators chase down several brutals on the beach, tire tracks from the camera vehicle can be seen briefly imprinted in the wet sand.
Other mistake: The Amazon's queen says she pierced Dharma's chest with her spear/lance but he's shown dying from a side wound.