To me, I think they should grateful for the business they get and can't imagine them putting a "bolt limit" on purchases. That makes no sense to me. Being that there weren't to be extra charges for cutting (I don't get this either), why in the world would he charge you for 2 1/3 yds instead of 1 2/3 yds. Hey $6 dollars could be another 2/3 yds of fabric and you know how much fabric means to us quilters.
I would take the receipt in when the owner is there and say, "I was charged for yardage that I didn't not receive." Their reaction would tell me if I was ever going to do business with them again, let alone tell all my friends, relatives, neighbors, etc. about my experience there.