Continuity mistake: During the second solitary visit that the Native Girl pays to doctor Bwana, she has to hold him steady after he drank the torpedo juice. Her right hand is in a completely different position in the various shots, and she lets Buster Keaton go once but is still holding him after the cut.
Factual error: Rifles and more so, cannons of the type shown in the movie were not close to being invented in the 1500s.
Continuity mistake: In the animal mortuary, Robert Morse opens a refrigerator with two dogs in it as he reads from a book. When he returns to that same refrigerator seconds later, the dogs are gone, replaced by a crumpled white cloth and a cat. (01:01:30)
Other mistake: Dean Jones and Connie Stevens are riding in a gondola of a skyway ride at a seaside amusement park. The gondola they are in is obviously on a studio soundstage. It is much larger than the gondolas shown in the rear-screen projection. In addition, there are no riders in any of the other gondolas and the gears and cables of the ride make absolutely no sound.
Other mistake: FBI Agent Kelso believes a cat may be able to lead him to the location of a kidnapped bank teller. He has four other men trying to follow the cat. When Agent Cahill reports that he is stationed "west of Whittier Street," Kelso sticks an identifying pin on a large map but he puts the pin in a location east of Whittier Street.
Revealing mistake: When Phil kills himself by throwing himself off the roof, in the shot of him supposedly hitting the ground it is painfully obvious that it is a dummy. Not only does it hit the ground completely rigidly but the wig on it even noticeably flies off on impact.
Revealing mistake: During practically every scene with Dr. Nadir, the prosthetics to make his cranium look more 'alien' are visible. In particular, when the Queen realises he's been shooting down spaceships and not missiles and calls him a 'fool', at the back of the neck the line where the concealing make-up ends is evident. Throughout the rest of the movie the other Martians have similar if not even more obvious bald caps. (00:17:45)