They probably checked you in anyway and assume you actually stayed there. Once they did the minibar check, something was missing. Apparently they did not notice it from the last occupant.

So, you were charged.

It happens. As a freq travelor, surprised this has not happened to you before. In most cases, a quick call to the hotel should clear it up. In this case, it should be easy. Often the hotel just wipes it off but not sure if the customer is right or wrong.