How long have you had the card?
When you log in to aa.com, it should show you somewhere as a cardholder. That's what entitles you to the benefits, not whether you used the card to buy the tickets.
But that takes a while to register after you get the card (maybe after your first use? I'm not sure). So if you got the card very recently, that may be the problem.
Also, do you have your AAdvantage number on the flight reservation? If not, that's the problem; the Citi card benefits are tied to your AAdvantage number, so if your AAdvantage number isn't on the flight reservation (you'd have to be able to add it somehow later if you booked it with ThankYou points, I presume), there's no way to get those benefits because it can't connect to your card.