I take it you mean the store categories you created are showing in the side-bar even though there's no items in them and they no longer even exist?
That happens to me sometimes when I delete / create new categories, and usually reloading pages fixes it, but the best thing I can think of to do is go into the store settings for listing frame, tick the box to remove the sidebar from listings and save, then clear cookies and cache, sign back in add the sidebar back to the listing frame and see if that helps.
