All three of the songs have virtually nothing to do with the film, the biggest of them all being "Scooby-Doo! Abracadabra-Doo". The only song that had any kind of relevance was "Dig It Scooby-Doo" which was used a tad late, but the scene in which it could have been used when Scooby dug for the "X" was presumably too brief (although the song was never meant to be taken literally).
Disguises: Shaggy as a cracker; Scooby and Shaggy as hula dancers.
Why would Shirley have Scooby Snacks in Gnarlybeard's pirate ship?
Velma often refers to Fred with the wrong full name Fredward. Fred's real name is Frederick. This could be justified by the fact that this film is set in a separate universe.