On the riverboat, the sign for the saloon is incorrectly spelled "Salon."
Right after Scooby drops the anchor and stops the runaway airboat, his blue collar turns yellow.
When the witch makes Daphne disappear, she is standing on a wooden floor. When the rest of them examine what happened to her, they see footprints on a rug. There was no rug where she was standing.
As Shaggy is holding the door to Jeb's cabin open with his right arm, the shadows of him and Scooby on the floor doesn't show Shaggy's outstretched arm.