I would ask the owner to send me a two yard piece of the one that should have been two yards and tell her you will send her back the one yard piece. That should convince her you aren't just trying to be difficult.
And if that fails, I would let her know that you are involved in some quilt boards that you will be sharing your bad experience with, and naming the store. You have a duty to warn others when you know of a store that has a pattern of poor customer service.