After Shaggy opens the roof in the room with the huge mirror Fred's shirt collar is briefly white, before returning to it's normal blue.
After the unmasking scene, when everyone is shown at the sanitarium, the characters' places change abruptly.
When the gang is being chased by the dogs, Daphne disappears briefly, making it look like one of the dogs is only chasing Fred and Velma.
In real life, Niagara Falls is surrounded by two cities (Niagara Falls, New York and Niagara Falls, Ontario), not in a "middle-of-nowhere" woodland.
It is unknown how the Ghost was able to get onto the waterfall's crag in the beginning.
Officer Oldfield made it clear to Fred to turn left for Foster Road, yet he completely ignores this when he heads right just because the sign is pointing in the wrong direction.