I think if it were me, IF I ever went back to that shop, I'd watch them like a hawk. Every cut they make, have them REmeasure it and fold it right there and write down the price of it. Do that for every piece of fabric you buy. Yep, it will make them furious, especially if they're trying deliberately to cheat you. But remind them that is how you handle people who cheat you. Sheez... that IS upsetting. At the cash register, then, ask the cashier to call out each and every item BEFORE she rings it up.
I think I'd file a very detailed complaint, with copies of bills and everything, with your state's Attorney General. That way, if too many complaints ensue, there will be an investigation into their sales practices. You're probably not the only one this has happened to. There are bad eggs in every crate. Sorry this happened to you! It doesn't pay to be too trusting anymore. :(