Continuity mistake: In the episode of Scooby movies where they meet the Three Stooges, Fred says that Velma is missing and they need to find her. When they go off to look for her they pass a window. Fred first, Daphne, then Velma (despite her being the one missing!), Shaggy, then Scooby.
Continuity mistake: In the cavern, Scooby and Shaggy dig holes in the ground. The rest of the group notice a truck drived by the Pterodactyl going toward them. Discs and cassetes fall from it. The shot later, the stones behind them have disappeared and the pile of discs have a different shape.
Other mistake: When the Mystery Company find a torn paper in a coffin, it is written exo-6 and something else. They find later that exo is the first part of exotic. The way the paper was torn, you should be able to see the lower part of the missing letters.