The pirate ship is about to enter the cave when the camera cuts away, then cuts back to see the ship farther away than before.
Daphne's lips have no lipstick, when Velma and Fred comment on first seeing Skull Island. Just as Daphne turns her head to the others to question it, they return to being pink.
When Fred, Daphne, and Velma first board the ship, Daphne's scarf is missing.
Scooby should not be able to pick up the dry ice without suffering instant frostbite even if only for a second.
Shaggy's sclera flash white as he brings up his paper pirate hat to his head. His sclera are also white for a few seconds when he first puts it on.
Before the gang knock on Mr. Magnus' door and after the first time the butler closes the door, Velma's eyes are missing.
When Shaggy is walking by Redbeard's portrait, his animation is shaky, making it look choppy.
When Shaggy is making the paper pirate hat, his leg vanishes from behind the table.
The pirates cast their shadows on Shaggy and Scooby, who themselves have no shadows.
Neither Daphne nor Freddy move their lips when they say "moe".