Miscalculation is a miscalculation and someone is going to pay for it.
It was a simple process ... recount the fabric and find out which of you was correct.
It sounds as though this clerk thought you were arguing the price of the fabric, versus the real issue of how much fabric did you REALLY buy?
I DEFINITELY would have said something - - ESPECIALLY to the owner of the LQS ... after all, that clerk's miscalculation will cost the bottom line MORE than it will ever add.
At least, if you bring this matter to the owner, then depending on that response - - that would make up my mind about whether I would ever go in that shop again.