Right before the Mystery Machine runs into all the fish, when they turn the corner, you can see Scooby sitting up behind everyone. But he was on top of the other car at the time, as you can see immediately after. (It looks like they reused the animation of the Mystery Machine turning the corner and forgot to blank Scooby out.)
When Scooby searches through the pile of fish for Shaggy, his left arm turns green.
The zombies are carrying a paper that says "The Temple in the Hills." This wouldn't be necessary since they already knew where their hideout is.
When the zombies try to obtain the mask at the curio shop, the salesman says that "it was just purchased by a young girl." Considering this very generic description, they miraculously realized that Daphne had the mask.
After Daphne agrees to buy the golden mask, you see the gang leave the shop, Daphne is not carrying the golden mask.
In the car chase scene, when the Mystery Machine turns in Fishermans Wharf, you can see Scooby Doo in the Mystery Machine, however you also see Scooby Doo in the car with the zombies in the same scene.