Continuity mistake: Shaggy and Scooby stop to play a game of pool. When Scooby looks up and notices the ape head trophy has vanished, he has 4 of the balls by him, including the 6 ball. It cuts over to Shaggy, and he has the exact same set of balls next to him.
Continuity mistake: After Candy and the stunt man quit the movie, Mr. Maxwell says he has to withdraw his job offer to the gang as it's too dangerous. As the gang is shown, Scooby is sitting in front of Shaggy and Fred. It cuts to a close up of him as he gets excited about this, and suddenly Fred and Shaggy have vanished.
Continuity mistake: The Ape Man breaks the rope bridge that Scooby is on and it begins to fall. But by the Ape Man, the stakes holding the broken ropes are still in the ground at his feet. Scooby falls down and lands on a root, which bounces him back up where he punches the Ape Man. The stakes and broken rope have vanished.
Continuity mistake: The camera pans over the filming set and stops on the gang with Mr. Maxwell. There is a van behind them with the Ape Man movie poster on the side. The vinyl piece on the side of the van goes behind the poster and is lined up directly with the orange letters saying "EPI-CENTER FILM COMPANY." It then cuts to a close up of the poster and suddenly it has moved up on the vinyl and become smaller, lined up with the underside of "LOCATION No.2"
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: 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.