The characters holding the signs "Say hi to me Clark" and "Fly me to the moon" change between shots.
The sign in U-Boat's chair is not there when gets up, but reappears in the next scene.
The strange liquid that Daphne, Fred, Zip, and Colt found on the floor, is forgotten about during the final act.
The gang gets on board the Sly Star One by winning the last five seats in a lottery. However, Clark Sparkman's summary of the proceedings made it sound like each of the last five seats was won separately.
Shaggy's driver's license gives his name as Shaggy Rogers. However, Shaggy's legal name is Norville Rogers. His spacesuit similarly names him S. Rogers rather than N. Rogers.
Daphne is learning to drive the Mystery Machine while wearing heels - which would make driving more difficult. Perhaps that's why she has trouble with the pedals.
The "Drivers Test" sign is missing an apostrophe.