Captain Cutler shoots two harpoons with chains attached into the back doors of the Mystery Machine. The Mystery Machine tries to drive away, but Captain Cutler holds the chains to prevent their escape. Freddy then reverses and knocks Captain Cutler into the water. As the Mystery Machine drives off the chains and the harpoons have disappeared from both the inside and outside of the Mystery Machine.
When Shaggy is flexing his muscles the refrigerator door is open and he's standing right in front of it but in the next shot when he throws the potion that Scooby made, the door is closed and he's standing off to the side.
When Fred is on the ground after being knocked off the motorbike during the joust with the Black Knight, he is still wearing the red neck scarf. When Daphne lands on the ground next to him, the red scarf is further away on the ground.
When the gang receives a fax on the results of the dinosaur scale, Velma takes it away from Shaggy and it appears that she is looking at one side of it. In the next shot the fax is turned the opposite way.
During the fight between the Black Knight and Daphne in Wickles Mansion, Daphne's shoes change. They start of as high heels, then they change to being flat and then with a slight heel all during the fight sequence.
When the control panel is in the air and Scooby tries to catch it, the Pterodactyl ghost comes flying by, tries to catch it too, and crashes with the Tar monster, which was standing close to them. But when Scooby presses the button and the monsters are destroyed, the Tar monster is across the room, holding Daphne, and the Pterodactyl is no longer stuck on him.
When scooby is spraying the monsters with a fire extinguisher in the final scene, he is shown freezing the tar monster then breaking through him. When he is flying through the air to get the control panel, you see the tar monster unfrozen and perfectly fine as the pterodactyl flew into him.