Continuity mistake: At the start of the movie the mystery machine drives through the wall once they have caught the ghost and the front is all dented up. A few scenes later it's perfect again.
Continuity mistake: At the end Rowan Atkinson is released wearing dishevelled clothes, long hair and a beard. When Scrappy is placed on the helicopter, he's standing behind the gang, clean shaven and wearing the clothes he was wearing when the robot controlled version had Scrappy inside.
Revealing mistake: After the little Scooby-gang has crashed through a window after being chased by monsters they bounce upon an awning and you can see that the glass from the window is now paper.
Continuity mistake: When they all are driving in the Mystery Machine, Scrappy pees on Daphne, and gets kicked out of the car. When you see him get kicked out, his bag is on the ground. But if you look carefully, you can see that the bag is on the ground before they even open the door to throw Scrappy out.
Continuity mistake: Within the first few scenes, which are apparently on the exact same day, and even in the exact same hour, Daphene's dress changes styles. For example, when she steps off the plane, she is wearing a purple minidress, with a low collar. But, a couple of minutes later, her dress suddenly has a noticeable hem, and a weird decoration thing at the bottom of her slightly lower low collar.
Continuity mistake: When Daphne is fighting on the roof with the wrestler, you can see the lever in the background which Daphne is supposed to pull. Above the lever is a sign which says "CAUTION - Clear vents before opening." Throughout the fighting scene the branches/vines that are beside the sign constantly go from hanging over the sign, to beside the sign. (01:09:00)
Continuity mistake: When we see the very first close shot of Emile Mondavarious' desk, the black lampshade on the desk is very close to the books that stand on his desk. Yet when we see the desk in the background, when Emile is talking to Scooby, the lamp has moved much farther away, and in the space that it has moved away, a figurine has appeared too. (00:57:45)
Revealing mistake: When Daphne and the wrestler are fighting on the roof, Daphne slams the door into the wrestler and the wrestler's head smashes through the door window. The wrestler then grabs Daphne's arm, and smashes his arm sideways into the doorframe. If you look closely, you may have to watch a few times, you can clearly see the pre-cut line that makes the doorframe easier for him to smash. (01:09:40)
Continuity mistake: The density of the monsters change during the movie. The first monster we see is so much lighter than Scooby that it gets catapulted hundreds of yards when Scooby falls from the bent tree. Later, the monsters are so heavy they crash through an awning that Scooby (and Shaggy, Daphne, and Mary Jane) had just bounced off of.
Continuity mistake: After the scene where the gang has each other's voices, they are seen walking to the Voodoo man's house because they hear an explosion. Fred is holding Daphne's purple purse in the forest, then he isn't carrying it at the Voodoo man's house. Then in the next scene, Daphne has it back again.