When Shaggy discovers the real Mondavarious at the end of the movie he has long shaggy hair and a full beard and mustache. When the gang walks outside the cave to the cheering crowds, Mondavarious is clean shaven and has a haircut.
In the opening scene where Daphne has been captured by the Luna Ghost we can distinctly hear her shouting for help and complaining about the ghost grabbing her. This is almost immediately prior to her release and the unmasking of the Ghost. She says later on that she was captured for nearly an hour and a half but about the time Fred tries to use the hose and gets knocked over, we see Daphne has been gagged with her own scarf so how could she speak earlier?
When Shaggy is skateboarding, Scooby grabs the hook to save them from being squashed by the machine. Right after they jump off the skateboard you can see the skateboard fall off the conveyor belt. It then reappears on the belt a second later to be squished.
When the monsters take over the hotel, Daphne is wearing a purple v-neck dress and hides the Daemon Ritus in a simple purple handbag. When they wake up on the beach, she's wearing a light purple halter swimsuit and is carrying a light purple beaded handbag, and she never had time to change. When Fred's protoplasm head enters her, she is wearing her dress again.
When Daphne kicks Zarkos into the vent, her shoes change from go-go boots to flat boots. The go-go boots are seen when she kicks him into the vent, but when she lands back on the other side of the ropes her boots are flat.
After Scooby's protoplasm is taken during the sacrifice, a henchman stands behind an unmasked Shaggy. In the very next shot, the same henchman walks to get behind Shaggy, who is in the process of unmasking himself.
When the gang split up in the castle Daphne heads for the exit as Fred said but after Scooby pinches Shaggy Daphne is seen back in the room where the gang split up and heads towards a door of one of the rides.
When Daphne, Shaggy, and Scooby are going into the castle, Daphne bribes Scooby with a Scooby snack that she pulls out of her purse. However, towards the beginning of the movie, it is made clear that none of the members of Mystery Inc. were aware that they were all invited to Spooky Island. Since they weren't aware they were all invited to the amusement park, Daphne would not have known that Scooby would be there and therefore would probably not have any Scooby snacks in her purse.
When Velma falls while catching the Luna ghost and starts hanging, her skirt is stuck to her legs even though shes upside down. The character of Velma Dinkley is NOT a flip-skirt girl. So they taped the skirt to Linda Cardellini's legs to prevent Velma's revealing her underwear.
The goof items below may give away important plot points.
When Mondavarious is talking to the gang as they walk along the ferry dock, they look at a line of students waiting to board the ferry to leave the island. All the students are acting like zombies, except the second one in the line. This boy appears to move his head to keep eye contact with the camera and nod his head in agreement with what Mondavarious is saying.
Shaggy should have no reason to know that Daphne's protoplasm has been extracted. (This is explained in a deleted scene where he sees them doing it to her. Since that scene isn't in the final cut, Shaggy shouldn't know she's been possessed.)
It seems that it is unnecessary to go to the trouble of setting the trap in the cave. The same objective could be accomplished by spilling the vat in the middle of the day, when all the students are outdoors. Velma's head has shown us that the heads are capable of flying to other parts of the island to find their bodies.