I am frequently a victim of the phantom minibar but cant really complain as I do tend to move the contents around sometimes to fit in a pint of milk - I hate UHT, but can't start the day, or function during it without my mug of tea and regular refills, I am such an addict I bring my own mug... So I suppose I deserve my phantom minibar, luckily its always taken off at the end of the day when I share my happy addiction with the FD...
I can't comment whether this is a frequent problem therefore because I may well be the cause due to my own activities, although these days some hotels leave an unused area of the minibar for personal use, thereby ensuring I don't need to move around the contents. Even so I still usually face the phantom minibar.
You should certainly take this up with management though, it smacks of fraud to me, I cant see how it could possibly be a mistake in an unoccupied room, that they know full well went untouched...