Wow, that shop sounds pretty shakey to me. I have done BOM at my fav lqs, and never had a problem. But a friend who did one at another shop in town had to nag the owner for fabric that was missing, pattern pages missing, etc. I think it sounds like your lqs is making their own copies and just being sloppy about the fabric. So sorry for this bad expericence, a BOM can be a great way to learn and finish a big quilt, don't let this turn you off.
I did get some photocopied instructions for one of my BOM, but I think that was the plan for the distributor because it was only a buck a block so I would think costs would be kept to a minimum.