I believe that stores of any variety will continue to do things the customers find questionable until someone (or more) complains about it. Before creating too much of a ruckus, you might ask the owner of the LQS about the extra charge. I remember taking a class one time and the students all needed a special variegated thread for the class - which we purchased at the LQS. The owner mis-read the invoice for the thread and charged us each the box price for the thread instead of the individual price. When it was pointed out to her the thread was VERY expensive, she found the error, admitted the mistake and gave each of us a store credit for the overcharge. Problem solved. To my knowledge, this did not happen again. I believe it was an honest mistake.