Very similar to my favorite local hardware store. I experience the same problem as the OP and the only way to solve it is to carefully check your bolts to make sure they are just what you need.
I usually buy at least a few spares because buying another .13 bolt is cheaper than having to drive back to town when I drop it down a gopher hole!
Just out of curiousity - at the small hardware stores that you guys (and I'm just speaking in general) - do they charge by the piece or by the pound? My favorite store charges by the piece, the other store I go to charges by the pound. I've never checked to see if there is much difference, but I know that their prices "per box" are comparable.
(By the way, both stores charge by the pound for nails/drywall screws/deck screws/etc. I'm talking about nuts, bolts, washers, etc. - just general threaded fasteners).