I have had fabric substituted but I was told about it. You can print out this thread and take it to the LQS and see if that makes a difference. You can also explain that (if you belong to a guild, club, church group, etc...)that you will be bring this problem up so that others will be forewarned to double check any kit they receive in the future before paying for it. YOu can also remind her that you can do BOMS from online vendors and that you don't have to do business with that shop. That's hardball I know but if you are really upset then...
On the other hand, I found out two things recently which makes me wonder how in the world, LQS can even do BOMs anymore. One thing I found out is that the middlemen that the LQS order from hold onto their orders and do not place them with the fabric companies until they have enough orders to make it worth their while. By that time, the fabric is gone because the second thing I learned is that smaller LQS may order a whole fabric line but they only receive a few bolts of a few fabrics regardless of what they order because of competition from places like Keepsake Quilting. If this makes a difference, then maybe, you can talk to the owner about this and still come to some mutually agreeable solution. Good luck and sorry this happened to you.