This is one of the many reasons I have almost completely stopped shopping at places like Hancocks. I shop almost exclusively at my LQS or at a few other LQS's in towns hubby and I travel to often. Good customer service and getting what I pay for is important enough to me to spend a little more per yard on quilt shop fabric.
I do also shop online and have been happy with several sites. Fabric.com is good and for batiks I LOVE batiksplus.com. Last year I had exceptional service from Fortworthfabricstudio.com. I also really like Connecting Threads, though I haven't ordered a lot of fabric from them because I'm usually looking for something pretty specific. I've been eyeing several of their new collections lately though. :)