If you take the fabric and your complaint to the store, they will just tell you "sorry, that is the way they come to us, I can't do anything about it" Translation: you are just screwed. So, how do you get this fixed? It will take some time but I have good results in the past.
Write a letter to Joann Fabrics, Customer Service. Describe the situation just the way you did on the QB. Request a refund or replacement fabric, hopefully you still have a receipt or some kind of paperwork. And this is the important part: You address the letter to Joann Fabrics but you also CC: (1) your local Consumer Protection Agency; (2) the State Consumer Protection Agency (3) the Federal Consumer Protection Agency (4) the Better Business Bureau in your area, (5) the Consumer Fraud Department in your area and (6) any other agency that you think would freak-out the Joann Fabrics Customer Service Department. It will take a little research to gather the addresses or email addresses from the internet but I know from past experience that they will have to address your complaint. They do not want to be contacted by any of those agencies and have to tell them they are ignoring the situation. I know the dollar amount is not in the hundreds, but if they are shortchanging the consumer with fat quarters, what other items are they shortchanging the consumer with?? For me, it is the principle of the thing. You should be able to use all of what you pay for. Probably won't change much in the long run but it's worth a try. Good luck. Finally, that is why I shop almost exclusively at LQS for my fabric - they know how important an exact measure of fabric is.