In the supermarket scene, Crunch and Brunch are clearly seen running out with Shaggy in the trolley. But in the next shot, Crunch is just walking along, looking up at the sky. In the next shot Crunch appears, he's back pushing the trolley again.
When Shaggy and Scooby try to escape from the castle, Scrappy ties the bedsheets to the bedpost so they can abseil down the tower. But, moments later, Shaggy scrambles back through the window after spotting the crocodile and the sheets have disappeared.
On the morning before the race, Crunch and Brunch enter the "ghastly room" and the door is too high for its frame. Not only that but it's changed colour, from brown to purple. These mistakes are also noticeable on the morning of the race.
After "disabling" the Werewolf Wagon, Brunch's monocle changes from being on his right eye to his left for a few scenes.
When Shaggy, Scooby, Googie and Scrappy first arrive in Transylvania, the thin witch speaks with a high, squeaky voice, but during the race, her voice is deep and gravelly.
At the end of the movie, when Shaggy turns back into a human, his girlfriend hugs him. During the animation of being hugged, Shaggy has part of his head from the previous animation frame shown at the same time.
When viewed on certain displays or monitors without overscan, in some shots of characters in a vehicle, the drawing of the vehicle is cut off near the bottom, revealing part of the background.
Shaggy's eyes turn white when he looks down at Scooby after he told Shaggy about Brunch and Crunch attempting to turn him into a werewolf.
When Scooby, Shaggy, Scrappy and Googie get trapped in the cage, the bars are wide. Scrappy could've easily walked through the bars since he's small enough.
When the cook at the drive-in theater snack bar asks Shaggy what he wants, Shaggy is in his werewolf form, but the cook does not seem to notice, and he acts surprised when he first hears Shaggy's hiccup-induced transformation into his human form. It isn't until the cook gives Shaggy his order when he finally realizes Shaggy is a werewolf and panics.