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.
Right after Scooby drops the anchor and stops the runaway airboat, his blue collar turns yellow.
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.
After catching the fish, Scooby-Doo is drawn larger than the van windshield.
On the riverboat, the sign for the saloon is incorrectly spelled "Salon."
Scooby would've just got out of the money sack he was in when it got caught on a piece of wood in the ground and wouldn't have fallen into the trap with the Witch and Zombie.