Continuity mistake: When Daphne jumps off the stairs to help the park owner her boots clearly change to trainers in mid flight and then back to boots when she lands.
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.
Continuity mistake: At the end when Mary Jane grabs Scooby and Shaggy by the neck and holds them off their feet, she grabs Shaggy with her left hand, in the next shot it is her right hand holding Shaggy's neck (you can see her turqouise bracelet) then back to her left hand.
Revealing mistake: When Scooby, Shaggy, Mary Jane, and Daphne go crashing through the window while running from the two monsters, the falling glass and broken window frame pass right through the CGI Scooby.
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.
Deliberate mistake: In the first scene Velma got sprayed by the hose and slips but gets her foot caught on the chain; hanging upside down, but her skirt doesn't go "up". Deliberate to maintain the "family movie" tone.
Revealing mistake: When the gang and Mary Jane are being chased down the corridor and jump out of the window, you can see that it isn't Daphne that hits the awning. It's a man in a dress.
Revealing mistake: When the monster that got into Daphne is being destroyed by sunlight, everything else in the room seems to have frozen for a second. Carefully look at Daphne.
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: At the airport before their flight to Spooky Island, Daphne wears a pink minidress and pink boots. This changes to black trousers. In the next scene in the plane, she wears her boots again.
Continuity mistake: In the final scene between Shaggy and Scooby, when they are gorging themselves and eating hot peppers, when the camera switches to the shot of only Scooby, the girl at the table behind him keeps appearing and disappearing.
Continuity mistake: When Scooby-Doo and Shaggy are being attacked by the food, there is a strand of "sausages" that has broken from around Scooby's waist. After the wall falls in the next scene it is back around his waist.
Continuity mistake: In the first scene when Velma is explaining how the Luna Ghost is able to fly, she hits the button that inflates the balloons with her right hand. When the shot changes, she is shown hitting it with her left hand.
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 Daphne jumps out of the pyramid as it is closing, the distance she has jumped changes between shots, and technically she should have been trapped halfway.
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.