Velma usually doesn't wear lipstick, but she is in this one. That is, until she explains the player-piano to Shaggy and Scooby, and the lipstick is gone.
When the gang opens the safe inside the old hotel, revealing the secret elevator, they are standing inside a large lobby. But when trying to coax Scooby into the elevator with Scooby Snax, the lobby has disappeared and is replaced by a wall.
At the end of the mystery, while the gang explains the investigation to the hotel owner, Scooby takes the Miner 49'er's stilts and uses them to reach apples from a tree. There is a water trough behind Scooby when he is putting the stilts on, but when the gang looks over to see him picking apples, the trough is gone, but it then reappears when Scooby steps in the gopher hole and falls in it.
When Shaggy pushes Scooby-Doo inside the lobby of the abandoned hotel, Scooby's black spots disappear, then reappear in the next shot.
When Daphne falls into a mine shaft Fred turns his head 180 degrees.