I think this has been brought up before, but it is still present in 3.04-2. Food in some stores will spoil and after a while all that is for sale is a bunch of spoiled food. I'm not quite sure what affects it, as some stores spoil while others are fine. It could be that the ones that you visit more spoil, but I'm not sure how the stores are stored when you're not there.

I just checked a bunch of sartolais villages (which all had granaries, for some reason), and 3 out of 5 granaries were spoiled. The one in the village that I visit often was completely spoiled (it has the local healer) and the other two that I had visited several times had a couple unspoiled items. The other 2 granaries I hadn't visited in a while and they didn't have any spoiled goods.