Even with this annoyance my LOVE for the Kimpton is still strong!
The OP (SJC AA) has it right:
This points to a combination of problems:
Poor inventory control -- items already missing before guests arrive
Poor customer service -- no proactive notification of item found missing
I have found spoiled leftovers still in the fridge from a previous guest (I assume this means that the inventory was not checked.) With dozens of variously shaped items in the minibar offering/basket I totally understand how mistakes can happen.
Some method of notification of the charge would be great. (Along with online printing of folios.)
I just ran the numbers and this happens to me on 6% of my stays.