Deliberate mistake: In the first scene Velma gets 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. (00:02:40)
Continuity mistake: When Shaggy and Scooby, stuck in the barrel, jump on the skateboard, they re-skate the same path. You can tell this because they pass the skateboards, boxes and the plastic yellow item that's under the conveyer belt twice. (00:02:45)
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 Velma inflates Old Man Smithers' suit, as the suit inflates, his arms raise. His left arm is raising in front of Velma, yet when it cuts his arm is now behind Velma. (00:05:10)
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. (00:05:22)
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)
Visible crew/equipment: During the film, set lights and reflectors can been seen reflected in Daphne's sunglasses and Velma's glasses numerous times, especially in closeups. (00:16:15)
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 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. (00:29:30)
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 Velma is sitting at a bar, about to investigate the artifact Daphne found, as it opens Velma brings her maginfying glass well away from the artifact twice between shots. (00:35:55)
Continuity mistake: When Velma is searching for her glasses during the monster attack in the bar, you see her friend in the Led Zeppelin top run away. Then the camera changes, and he is hiding under the bar again. (00:40:04)
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. (00:40:50)
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. (00:42:30)
Continuity mistake: When Scooby, Daphne, Mary-Jane and Shaggy are being chased by monsters and crash through a window off the luggage cart, the window is already broken before they make impact on it. (00:42:30)
Audio problem: When Daphne, Mary-Jane, Scooby and Shaggy awake on the beach, they walk off into crowds of people playing and partying. Shaggy then says "Does anyone else think this is strange?" Shaggy's mouth doesn't move at all to this line though. (00:45:30)
Revealing mistake: When Fred smashes his arm through the round window of the garage and grabs Shaggy, if you look you can see some kind of clear tape on his arm to protect him from the glass. This is quite noticeable in closeups. (00:47:10)
Visible crew/equipment: When Shaggy and Scooby are riding the quad bikes, they stop to pick up Mary-Jane. They then ride off, and one man jumps athletically into the air, to try and catch them, revealing knee-pads under his shorts to protect him when he falls to the floor. (00:48:10)
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)
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. (00:53:50)
Answer: It's never mentioned where they went afterwards.
MasterOfAll