There are a lot of stores in my area that have built up a huge craft beer section. The problem is that the stock just doesn't get turned over. I've stopped buying APA's/IPA's unless they have a "born on" date within 2-3 months, or they are a current seasonal release. I actually have better luck at stores with a small selection because I know that the common stuff like Harpoon IPA, SNPA, etc. gets turned around pretty quick.
I had the same issue with my local beer store, to the point that I won't buy ANY beer from them unless its date stamped. They have a huge selection, and a great staff, but it seems that nothing ever gets tossed. They were kind enough to order me a Stone beer I had brewed a clone of a while back that isn't available in our area. I went in and picked it up, and it was a year past the "best by". Huge chunks of proteins floating around in it, really nasty. So in that case it's not just the store, but the distributor as well. They did refund my money, however. "Meijer", which is a Midwestern mega-grocery store chain out here, now has an entire MI/Craft beer section with a high turnover of product, and as much as I want to spend my $ with the little guys it's hard to turn down fresh beer at a better price.