It can still be rational, but you need to look at shopping as an aggregate of probabilities.

Let's make it more extreme. A $50 item for free or $50 off a $5000 purchase. Discounts as big as 100% off don't come every day. Maybe you'll never see that deal again in your life. You should jump on it. Where as a 1% discount is something you see every day at dozens of stores. There will probably be a bigger discount next week, so don't bother going out of your way.

If you have to make a choice between the two, you choose the item with the less-common discount.