I have a persistent problem with my shops behaving like there is no stock when there is stock. As far as I know, this has only been happening on shops with one item in. I have shops that I use for special, uniquely named enchanted gear (eg top enchanted picks or boots or bows etc) with only one item in stock at a time. But people have been having trouble buying them because the game tells them the shop is out of stock. The only way to sell it has been for me to break the sign and make the shop again, while they are there, and then it has worked. I can only guess that people are trying to buy stuff when I'm offline and not being able to. It's happened many times while I am online.