My harbor resources is at level 16 that is at 14,000 (FREE FOR RAIDS) for all three resources.  My warehouses are at max at 13,925. My rum cellars are at max at 13,925. 

When a raid happen, I lose 1600 in resources. I check my past action reports, each raid cost me a  5 percent LOSS. 

The problem is if the harbor storage is higher then both warehouse and run cellar, WHY IS THERE A LOST in resources ???????