When Jack is talking to Mr. and Mrs. Johnson about buying their house and tearing it down, the scene cuts to Scooby, Daphne and Mr. Boo looking surprised. At this shot, Mr. Boo is suddenly opaque, rather than semi-transparent.
Although the detectives interact with a real ghost in this one, the rest of the series has to go back to them not being real. This can be partly excused through Daphne, who still denies their existence even with living proof (so to speak).
Scooby and Shaggy's Commander Cool and Mellow Mutt costumes are red and yellow, instead of blue and white. Shaggy's glasses and Scooby's mask are missing as well.