Fred is wearing his Pajamas when he goes into the bathroom to inspect the bathtub that Scooby was in and finds it bolted down. In one shot, he's wearing his regular shirt and scarf and in the next shot of him, he's wearing his pajamas again.
When Velma tells Shaggy to follow the Phantom Shadow's footprints, her glasses have no lenses or the tint is missing from them.
When Scooby is trying to tell Shag and Fred about the bathtub tipping into the basement, Fred is wearing his regular clothes, when he tells them to look in the bathroom instead of his pajamas. Also at this time, the front of the fish food box has no writing.
Fred is wearing his normal clothes and not his pajamas when the gang peeks out their rooms after they hear spooky noises coming from Cousin Simple's room.
When Shaggy takes out his sandwich, the fishbowl beside him is completely empty, no water or fish. But a few seconds later, when he grabs the box of fish food, the bowl has water and a goldfish that bares teeth and snaps at Shaggy! The fishbowl is empty once again when Shaggy repeats back to Scooby about the bathtub being dropped into the basement.
When Velma is running from one of the Green Ghosts, a phone rings and she picks it up. Why would anybody be calling the mansion if nobody lives there anymore? (Perhaps it was a nuisance caller, a wrong number, or, as it sounded, one of the phantoms.)
The gang did not come with any luggage, yet Shaggy and Fred later have their pajamas.
They did however come with a Van.
Scooby, Shaggy and Velma are on a drainpipe that breaks, throwing them into a cave. But the drainpipe falls on top of, instead of in, the water as if the ocean were hard ground.
When Velma says how Shaggy and Scooby are watching on the drainpipe, one of her arms is missing.
When the drainpipe is falling towards the ocean, the pipe hits the ocean like it is glass. There is no splash.
The flying bone isn't explained. One can only imagine that the mansion really is haunted.