Unless some effect has specifically ordered a portion of the deck (Phoenix Wing Wind Blast sending a card to the top of the deck, for example) then the deck was random to begin with. Random is random. Give a Procedural Error- Minor (shuffling deck) - Warning ...and move on.
If a card(s) were placed on top (or bottom, etc.) of the Deck and both have knowledge of the card(s), replace them in their appropriate order after shuffling. If cards were placed unknown to one player or the other, the HJ's discretion must be used to determine the extent of the damage to the game state (to some degree weight must be given to whether the shuffler would necessarily gain an advantage by shuffling cards he had seen via an effect such as, say, Fruits of Kozaky's Studies). For the most part, though, it should be repairable in most situations.
I want to fix the game state.
I must fix the game state!
Please! Please! Let me fix the Game State!!!