I had an issue with my Joann's recently also....I had 2 coupons and one was 50% off a reg. priced item and one was 40% off. They told me I could use both, so I handed the young girl both. She fiddled with the register a while and then told me my total. OK. I thought it had taken both coupons as she kept them. Well, I got home and she had only put in one. I was pretty chapped, but it was a small amount I purchased. Had it been a large sum, I would have been back in the store. Usually I do not have a problem with the regular cashiers, but I had never seen this one before. Maybe she was new and didn't know how to do it, but she should have called someone over.
Sorry this happened to you. They usually take other store coupons at my Joann's though. But it's the "regular" cashier that does it the best and most honest way.