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.
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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.
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.
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.
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.
Continuity mistake: When Scooby Doo and the gang are pursued by the invisible ghost with a candle, they hide in a room and Scooby blows out the candle and shuts the door. You can see the door has a handle on the left hand side, but when we see the gang in the room in the next shot, there is no handle on the door.