- Continuity: Daphne runs up the framed stairwell wearing tennis shoes instead of the pink go-go boots she wears throughout the rest of the movie (see also trivia).
- Continuity: When Mary Jane grabs both Scooby and Shaggy while they were escaping from the bad guys, the hand she is holding Shaggy changes from the left to her right after she breathes on him.
- Revealing mistakes: When Scooby punches Fred on the airplane, Fred moves his head before Scooby makes contact.
- Continuity: When Daphne first meets the voodoo guy he is barefoot. In the next shot he's wearing shoes, and in the shot after that he's barefoot again.
- Continuity: At the sacrifice, just after Shaggy is revealed, there is a henchman standing behind Shaggy. In the very next shot, the same henchman walks to get behind Shaggy.
- Continuity: in the beginning when Shaggy is skateboarding, Scooby grabs the hook to save them from being squashed by the machine. Right after they jump off the skateboard you can see the skateboard fall off the conveyor belt. But then it reappears on the belt a second later to be squished.
- Continuity: When Scooby and Shaggy are in the building with the quads, the rock band comes in and breaks a window. In the next shot, the glass is broken in a different way.
- Continuity: When Fred comes in the woods with Daphne's voice, he's carrying Daphne's handbag. When they see the voodoo man for the second time, Fred is no longer carrying the handbag.
- Continuity: When Daphne, Shaggy, and Scooby were going to the castle, she was carrying her handbag, but while trying to open the door on the ride, her handbag is clearly gone.
- Revealing mistakes: During the BBQ scene in the van, even with the roof vent open, the van would be filled with thick toxic smoke. Also, the space in the scene is wider than the space in the back of a van.
- Revealing mistakes: When the park owner is talking to Velma as they walk along the ferry dock, we see a line of students waiting to board the ferry to leave the island. All the students are acting like zombies, except the second one in the line. This boy appears to be moving his head to keep eye contact with the movie camera and he is nodding his head in agreement with what the park owner is saying. After the van crashes into the factory building, there is no damage on it, not even a scratch!
- Plot holes: It seems that it is unnecessary to go to the trouble of setting the trap in the cave. The same objective could be accomplished by spilling the vat in the middle of the day, when all the students are outdoors. Velma's head has shown us that the heads are capable of flying to other parts of the island to find their bodies.
- Revealing mistakes: In the scene were Scooby is pushing the cart of luggage with the gang on it, a pulley system is clearly seen pulling the cart. This chord disappears and appears randomly throughout the scene.
- Audio/visual unsynchronized: In the opening scene where Daphne has been captured by the Luna Ghost we can distinctly hear her shouting for help and complaining about the ghost grabbing her. This is almost immediately prior to her release and the unmasking of the Ghost. She says later on that she was captured for nearly an hour and a half but about the time Fred tries to use the hose and gets knocked over, we see Daphne has been gagged with her own scarf so how could she speak earlier?
- Boom mic visible: When the mystery inc. meets again on the airport after they split up, you can see four times a studio mic hanging in the picture. First, when Fred is talking to Velma when she told him that she works for NASA you can see the mike hanging in the middle of the picture, then it gets moved a little higher, then reappears. When they see Daphne moaning at the check-in you can see the mike again first in the top-middle of the picture and then much bigger a few seconds later in the top-right corner.
- Continuity: In the last scene where Fred is talking to the press you can see him holding the daemon-ritus in his left hand in a glass casing, in the next shot the case is gone.
- Continuity: The person standing next in line, waiting to leave spooky island as Mystery Inc. arrive, suddenly has glasses, then loses them, then has them again.
- Errors made by characters (possibly deliberate errors by the filmmakers): When they arrive on Spooky Island, the place is crowded with spring break college students. The owner also states that the place is a leading place for students to go on spring break. Ergo, the film takes place in March. However, the voodoo man claims it is the middle of May.
- Incorrectly regarded as goofs: When Velma falls while catching the Luna ghost and starts hanging, her skirt is stuck to her legs even though shes upside down. The character of Velma Dinkley is NOT a flip-skirt girl. So they taped the skirt to Linda Cardellini's legs to prevent Velma's revealing her underwear.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Continuity: SPOILER: When Scrappy is a huge monster the pyramid-shaped "plug" disappears and then reappears again between shots before it gets removed.
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