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.
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.
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.