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.
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.