What a Night for a Knight - S1-E1
Plot hole: It seems unlikely that: 1. The curator, who's short and chubby could fit into that suit of armor. 2. How he could be strong enough to lift up the table Scooby and Shaggy are hiding under at one point, 3. That the museum has no security guards who might catch the curator and his thugs during their art forgery scheme and 4. There are eyes shown moving in the suit of armor when the gang's talking to the curator despite the fact he's the Black Knight Ghost.
Plot hole: Given he fell down into a ravine it seems impossible for Carl to have got back to his trailer before Mystery Inc does.
Scooby-Doo and a Mummy Too! - S1-E12
Plot hole: If the guilty man knew the diamond scarab was in the hippo statue then there's no reason he couldn't have broken the statue open and taken it.
Chosen answer: A ghost wouldn't have to keep any food in the fridge - they don't need to eat. So it is one thing that proves the ghost is not a ghost.