Continuity mistake: In the beginning of the movie during the skateboard scene with Shaggy and Scooby riding along the conveyor belt, Scooby grabs a hook and both Shaggy and Scooby jump off of the skateboard. You see the skateboard falling off the conveyor belt, but in the next scene it is on the conveyor belt and being crushed. (00:03:20)
Continuity mistake: When the monster comes out of Daphne's body, Velma runs to the window and her right hand is about to open the blind (she holds the string). When the shot cuts to Daphne, we can see the lower part of Velma's body in the background with both of her hands down (doing nothing). When the shot cuts to Velma again, her right hand is up and about to pull the string. (00:53:35)
Continuity mistake: When Scooby-Doo falls down the hole to the cavern below Shaggy follows him a few seconds later. When Shaggy hits the sand below he has to roll when he hits the ground. In doing so, his back and knees are covered in what appear to be thick sand deposits. When he stands up in the next shot and turns around he has no sand on his knees or on his back. He has not made an effort to brush his pants or shirt off.
Continuity mistake: When Shaggy and Scooby are being chase by monster Fred and the Sugar Ray band, they enter the shed and Fred crashes his hand through the window and there is a large shard of glass under is arm, the shot changes and the shard is gone. Back to original shot and the shard is back.
Continuity mistake: When Shaggy and Scooby are doing the farting competition, Daphne comes and runs a good distance in front of the white/green wall on her left. After cutting to Scooby, we see Daphne walking out from the dark and passes the wall that she is supposed to have already passed. (00:33:20)
Continuity mistake: When the monsters all come out in the hotel at Spooky Island, Scooby hides under the table with Fred standing in front of him. The camera angle changes from a close up of the table to a long shot looking at the whole scene. When looking at the long shot, Scooby-Doo is not under the table but when the camera cuts back Scooby-Doo is still there as if he hadn't moved.
Continuity mistake: When the gang are at the edge of the woods staring at the voodoo man, and Daphne says she can handle him and walks towards him. When she takes a step forward you can see a light purple bra under a dark purple dress. A few minutes later the dress is pulled back up and the bra is no longer visible.
Continuity mistake: In the very beginning of the scene where Daphne motions Scooby and Shaggy over and ends up giving them Scooby snacks, there is a low shot from behind Daphne as she walks into frame. She doesn't have her purse. But the next shot is from the front of her, and motions for Shaggy and Scooby with her purse.
Continuity mistake: At the beginning, as the gang splits up, Velma says, "I'm outta here." In the shot facing Daphne, Fred is walking to his red car in the background and gets close enough so he is turning left towards the driver's side door. Then when Shaggy says, "No, don't go.", in the overhead shot Fred is much farther away from his car.
Continuity mistake: When Fred and Velma unexpectedly meet at the airport watch out for a long haired blonde guy carrying a surfboard who passes Fred twice. He also appears again a few seconds later behind Velma when she comments about how she's been working for NASA (he's wearing the same clothes but without the sunglasses or surfboard and is now reading a magazine). Then we see a frontal shot of Fred and Velma and he's now vanished.