This problem is not hard to solve when you limit physical access, i.e. in a warehouse, pharmacy, or locked room where multiple employees are responsible for checking in and out items. These solutions arose directly out of your conundrum in retail, and investigations are launched when someone discovers a mismatch between inventory and real life (think toxic chemicals, drugs, etc).
Of course it just so happens that nobody wants to go to a grocery store where they're not allowed to touch the items.