Factual error: Towards the end of the movie when Superman and Henshaw are fighting on the Watch Tower in space, Lois hits the sun shades to lower them so that direct sunlight can hit Superman and power him up. This is out in space with no atmosphere to filter the sunlight. The reason the blockers were there was for this reason, to keep the harmful unfiltered sun light from hitting people on the ship through the windows. However, she is able to stand there in the direct light after it's done and kiss and hold Superman without being hurt or burned by the intense direct unfiltered sunlight or its radiation.
Continuity mistake: Scooby and Shaggy are lying face down on the massage table when the zombies arrive. Shaggy has his robe lowered baring the upper back, but in the close-ups you can still see the robe up covering his shoulders perfectly. (00:28:00)
Other mistake: Throughout this, a running gag is that Fred can't drive stick/clutch. However, in "What's New, Scooby-Doo?" Series 2, Episode 6 "A Scooby-Doo Halloween," he yells at Shaggy that he's riding the clutch too hard at the beginning of the episode. If the Mystery Machine has a clutch mechanism, he would know how to drive stick/clutch.