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.
Revealing mistake: When Shaggy, Scooby and Mary Jane have escaped the monsters using the quad bikes, they land in a small pit and Scooby starts barking at Mary Jane. When Shaggy says, "Scooby-Doo like what are you doin' man", Shaggy is talking to the floor - he's not looking anywhere near the CGI Scooby.
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.