Are you guys using the Autolist feature? That can mess things up if you haven't set it up correctly. For example, before I realized how to use the Inventory auto-relist, I also listed items that I didn't have anymore, simply because I had put it into Inventory *after* I listed the first item. That way I had one item to much in Inventory.
It's also possible that you keep autorelisting it indefinitely, long after all your items are sold out. So, check what your auto-relist is set to.