You say this food was for your puppy, so I'm guessing this might have been your first experience in a pet store. Perhaps you are under the assumption that this is a unique policy, but I don't know ANY store that accepts coupons AFTER a purchase hase been made! It's probably much more likely that the first manager simply misunderstood your question when he agreed.
Hey, it's not like you can't still use the coupon, right? I mean, you still have the puppy to feed, right? Lighten up and give them a break!