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.
Revealing mistake: When the gang is chased out through the window, Scooby pushes them on a cart. During the shot, on the floor, you can see the tracks that the cart is travelling on.
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.
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.
Revealing mistake: In the little clip at the end, Scooby Doo opens a jar of peppers and dumps them in his mouth. You can see that there should be more in the jar than the seven or so that fall into his mouth, but suddenly the jar is empty.
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)