Continuity mistake: There is a scene in which a ghost shoots harpoons through the back door of the Mystery Machine. In the next shot, the harpoons are gone, and when the van gets back into the city you see a shot of the back and there is no damage whatsoever. (01:03:20)
Continuity mistake: When Daphne and Fred attach the jumper cable to the Black Night Ghost and the 10,000 Volt Ghost, they run away as the monsters explode. We see different shots of the monsters exploding and then we see Daphne and Fred in the corner running away a second time. It's the same shot as before. (01:12:10)
Visible crew/equipment: When the gang break into the house at the beginning we see Shaggy playing with an old record player. It suddenly turns on with a bang, and if you look quickly when the camera returns to Shaggy, you can see a hand on the left side of the screen (with what looks like the remote to turn the record player on) quickly pull out of view off screen.
Factual error: At one point in the film there is footage on the news of Mystery Inc's embarrassing attempt to stop the ghouls from stealing costumes. In particular, it focuses on Shaggy and Scooby being dragged across the table, etc. But look at the angle it's taken from: no one could have taken that.
Revealing mistake: Just after the pterodactyl ghost has been "tied up", it flies off. When Shaggy and Scooby are looking at the ropes, Fred and Daphne duck at the same time. Obviously it was meant to look like they are ducking when the pterodactyl's wings flap, but the pterodactyl has already flown off. (00:09:00)
Continuity mistake: When Scooby puts down all the stuff he found in Wickle's' manor and Shaggy says those are just stuff Scooby wants, the toilet brush is on the left for Shaggy and it's standing up. When Scooby picks it up, he picks it up from Shaggy's left side, while it is slightly lying down. (00:21:25)
Continuity mistake: When Velma is reading the inscription over the door of the "monster's hive", her hands are behind her back. Then the shot goes to Fred and Daphne with Velma in the background and her hands are down by her side. When the camera goes back to Velma, her hands are once again behind her back. (00:49:10)