I have run into this problem too. I wish Shopify would actually address this. Currently Shopify's order fulfillment is very buggy and frequently does not work as stated in their own documentation.

We have an item that is in stock at one location and out of stock at another location. Despite this, a customer was able to purchase 2 of these items to be fulfilled from the location with no stock. The 'available' inventory for this item is now show...