The display case, which had the Commander Cool comic book that Selma sold to Shaggy had only one comic book left after she sold the Commander Cool comic to Shaggy. Then later when Shaggy and Scooby return to Selma's booth, the case has two comic books in it.
The amount of bubble gum covering Dr. Croaker changes as soon as he's unmasked than there was when he was caught. There's less bubble gum when he's caught and more showing when he's unmasked.
The display case in Selma's booth has a padlock on it. But in the close up of her unlocking the case, the lock changes to an integrated lock. Then it's always shown as a padlock in the long shots.
Missing 3rd clue the part where Shaggy was grilling all of the suspects, How did McWendel know that Dr. Croaker attacked Shaggy and stole Shaggy's valuable collector's edition of "Commander Cool" comic book and Saying that's right, Shaggy can't be two people at once.