Scrappy-Doo was a character in the original "Scooby-Doo, Where Are You!" series and a few spin-offs, but he was not part of the "Mystery Incorporated" continuity.
"Haunted Museum" is an episode of the "Scooby-Doo Mystery Incorporated" series that features the regular Scooby-Doo gang: Scooby-Doo, Shaggy, Fred, Daphne, and Velma.
Therefore, Scrappy-Doo was not in the "Haunted Museum" episode.