I have an international flight with a domestic segment in three days. When I booked it in Y I requested a stickers upgrade for the domestic segment. Later I called and put myself on a waitlist for a miles & copay upgrade. Today the domestic segment was upgraded with stickers at T-72. Then I called the customer service and pushed through my international flight upgrade.

But the new ticket says that the domestic segment has fare code X, that is a stickers upgrade, instead of A. I expected that the domestic segment would be covered with miles & copay upgrade. That was confirmed by an agent who upgraded the international segment. However, when I called AA again I was told that since the stickers upgrade cleared first the stickers would be deducted from my account. Is it how it's supposed to work?