Unfortunately, this happens far too often even with quilt-shop quality fabric. I work at a LQS, and when we catch a flaw as we are measuring for a customer, we will cut around the flaw, using any leftovers as fat quarters or to put in a scrap bag. The fabric directly around the flaw goes into the scrap box that we use for making shop samples. This is a very aggrevating situation! Also, when the fabric is cut into two or more lengths in the middle of the bolt.
Occasionally, a flaw gets past us. If the customer brings it to our attention, we will make it good.