When Fred pulls the newspaper out of the barrel, Daphne says "Look at the story that's been circled" but when we see the newspaper, the story clearly hasn't been circled.
After Fred is rescued from the hook on the ceiling, his left hand is completely invisible for a few seconds and then reappears moments later.
The Air Force base has been abandoned for many years, but the dishwashing equipment in the mess hall is in perfect operating order.
When Fred, Daphnie, and Velma are about to go to the tower and meet Shaggy and Scooby, Fred notices the ghost trying to get there first. However, when we see the ghost running, he runs past the tower.
Shaggy sees Scooby's reflection in the window, but he doesn't see his own. Scooby was behind Shaggy, so Scooby shouldn't have been seen in the window at all.
Henry Bascombe: And I'da done it too, if you kids had'na come along!
Adapted twice into a comic book story, as "The Kooky Space Kook" (Gold Key #4, December 1970) and "Spooky Space Kook" (Archie Comics #20, May 1997).
The scene where Scooby and Shaggy lock themselves in a hut, Scooby throwing the key out the window, the ghost coming in through the other door, Shaggy and Scooby leaping out the window to retrieve the key and hop back in so they can unlock the door can be traced back to the Bugs Bunny cartoon Buccaneer Bunny (1946). A scene had Bugs rowing a boat to Pirate Sam's ship (the boat is tied to shore and is propelled back but Bugs treads water anyway). Sam boards the boat but sees the oars on the ship stairs. Sam swims out to the ship, retrieves the oars, swims back to the rowboat and rows his way to the ship.