Continuity mistake: The gang find Jonny tied up in a chair and he says it wasn't a publicity stunt. Both his arms are tied up to his sides by the rope. It cuts from the close up to show them all again, and suddenly Jonny is holding his hand to his head and Fred is suddenly pulling on the rope, his arm outside of the rope. (00:02:45)
Other mistake: There is a scene where the gang is the home of the Bank President, just after dropping off the injured bank guard. At one point the Bank President is standing behind an end table of some kind with a lamp on it. Even though there is nothing underneath the table to block your view you cannot see the lower part of the Bank President's leg. It looks like it has been cut off.
Continuity mistake: After the mystery is solved, the gang are driving away in the Mystery Machine. Shaggy and Scooby are in the back marveling at their wax dummies. Velma, Daphne, and Fred are in the front seat and can look back at them. But when it shows an angle from in front of them, the inside of the van behind Fred, Daphne and Velma can't be seen, only a solid gray wall where you should see Scooby, Shaggy, and their dummies, and even the back doors of the van. (00:20:50)
Continuity mistake: Fred begins telling the gang his plan for trapping the Wax Phantom. They are standing at a window with Fred on the right, Daphne in the middle, and Velma on the left with Shaggy behind them. It cuts to a view from behind, and suddenly Daphne and Velma have switched spots, and Shaggy is off to the side. (00:17:15)
Continuity mistake: In Mr. Grisby's house, Shaggy says "what a place to live," and Mr. Grisby is shown to be on the left side of him, Scooby and Velma with the crystal ball on their left. It cuts to a different angle as Velma says "it's a nice place" and Mr. Grisby is suddenly on the same side as the crystal ball with his hand on it. (00:05:30)
Continuity mistake: Fred is explaining his plan to check out the wax museum and Daphne is standing beside him. In the far shot she is facing him with her hand on her hip. It cuts to a close up of Fred and suddenly she is facing the same direction as him and has her arm down at her side. (00:04:20)
Continuity mistake: Right after the car chase when the Mystery Machine crashes into the boat and fishes, when Scooby reaches into the pile of fishes, his arm turns green. When he pulls out the fish, his arm is back to normal. But when he reaches back down it changes to green then back to normal when he pulls out Shaggy.
Continuity mistake: During the chase scene, we see the Fisherman's Wharf sign and then cut to the Mystery Machine turning around a corner. At this point, you can see Scooby is in the vehicle with the rest of the gang, but just a few seconds later he is back on top of the Zombies' car.