Are you using a regular coupon code in WooCommerce or are you using something like the bulk item discount plugin?
If it's the regular coupon code can you let me know exactly how to reproduce the problem? I think I've gotten this stuff fixed in my dev repo, but I'd like more samples to try and reproduce the problem to confirm it's indeed fixed.
If you could tell me the price of the item(s) you're adding to the cart and the type of discount you're applying that would be a big help.