I had this happen multiple times in Hancock Fabrics too. No where did I see a sale sign, but all the sudden the fabric rings up for between 20 and 30% so that I can't use a 40% off coupon. However, when I question it, they did override so I got the 40%...and proceeded to roll their eyes like I was the stupid one!
I think they hope the consumer won't notice. I know a lot of people who wouldn't be doing %s in their head and wouldn't notice til later (if at all). I think it is a deceptive practice and pretty much done on purpose.