I would say: "Why wasn't the mileage coupon applied to my plane ticket?"
I'm flying back to Russia for the summer, and I want to use a mileage coupon to get a cheaper plane ticket. I say to the travel agent:
How come the mileage coupon wasn't put towards my plane ticket? The cost has not changed.
How come the mileage coupon wasn't used on my plane ticket? The cost has not changed.
Are both okay?
So, mine are both nonnative?
The opener "how come" is a bit informal for a business transaction. "Put towards" would probably work. "Used on" doesn't work for me. But I prefer "applied to".