Continuity mistake: When the voodoo man is about to sacrifice his chicken and then Daphne walks in, the voodoo man is clearly barefoot. Then during the conversation between Daphne and him, when we see him fully again, he has sandals on. Then when Daphne leaves his hut he is barefoot once again. (00:20:40 - 00:22:00)
Continuity mistake: When Velma and Fred are walking through the airport talking, you can see there is a girl with yellow pants walking in the opposite direction with another person. However, when you see the crowd around Daphne as she is complaining about how the system is so economy, you see that part of the crowd is the same girl with the yellow pants.
Continuity mistake: Daphne wears three types of boots in the movie: 1) When she is wrestling with the blue costumed guy at the end, when she jumps over the railing to kick him, it goes to a close-up of her foot hitting him and the heel squishes in. (I'm assuming that this was done so as to not hurt the wrestler being hit with her foot. 2) Later, she kicks up and she is wearing pink flats. 3) In the rest of the film, she wears normal pink go-go boots with a solid heel.
Continuity mistake: When Shaggy and Scooby are in the Mystery Machine, cooking and eating food, someone knocks on the door of the van and Shaggy tells Scooby to "Grab the food." Scooby grabs loads of food, and we see two cans of Sprite which are stacked on top of each other, fall to the floor. These then appear back on the shelf on top of each other in the next wideshot, and fall once again! (00:08:10)
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.
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)
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.