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.
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.
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.
After Daphne fights the 10,000 volt ghost and gets hit way over to where Fred is, her hair is singed on the ends (as it would be). But when she and Fred meet up with Velma, her hair is normal again.
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.
In the 10,000 volt ghost and black knight scene, the explosion should have ruined the MYSTERY INC. car.
No news station would allow the reporter's edits of Fred's quotes to be aired as his quotes are deliberately taken out of context in order to defame him. This is textbook slander and would open the station to a massive lawsuit.
After Daphne gets blown up, the ground moves when she hits the ground, revealing that there's a crash mat there.
When Velma is watching the projection in the cave, the projector has no tape on it. The wheels are also spinning the same way, so no projection would actually be shown.
At approximately 1:01:21, Velma is shown using an E6B Flight Computer to do calculations completely unrelated to anything contained on an E6B.
When Fred is fighting the Black Knight Ghost in Wickles Manor, on the last blow before Fred is knocked to the ground, the padding on the back side of Fred's shield is visible as it descends.
After Fred and Daphne have fallen and the Knight Ghost approaches them, you can see a polka dot pillow underneath Fred.
The woman in the club who was dancing with Scooby doesn't recognize he's actually a dog especially when he barked a couple times while dancing and the way he talks.