When Scooby and the gang are getting dipped into the vats of Scooby Snack mixture, we see a close up of Freddy getting dipped into the vat. The mixture is orange when he gets dipped, but then in the next shot where the whole gang gets dipped and Freddy comes up, the color of the mixture on Freddy changes from orange to magenta.
After the gang gets dipped into the vats of Scooby Snack mixture, the mixture that got all over Shaggy is purple. Then in the next shot, it changes from purple to brown. Then the mixture on Shaggy changes back to purple in the shot of Shaggy, Daphne, and Freddy.
When the gang encounters Mr. Roquefort, Freddy discovers cheese on his shoe, Mr. Roquefort discovers cheese on Freddy and Daphne shoes. Earlier they didn't have any cheese on their shoes. Then when Mr. Roquefort runs away, the cheese on his shoes are gone. Same thing with Freddy and Daphne.
Mr. Roquefort has cheese on his shoes as Freddy discovers it. He didn't have any on his shoes before then.
At the beginning when Scooby is out of Scooby Snacks, Shaggy goes through every box they have. Then up to the point where Shaggy discovers they are completely out of Scooby Snacks, there are a bunch of empty Scooby Snack boxes on the floor. Then when Shaggy is coming down the ladder, all the boxes that were on the floor are gone and there are two empty boxes on the shelf.