How far in advance did you open the card? If it was more than 7 days before your flight, I would think that you could get a refund by submitting a request to Citibank customer service.
As someone else pointed out, your AAdvantage number had probably not yet been linked to the card by the time of your check-in. It may also be worth calling Citi be sure that it has been properly linked to your existing number and they did not create a new number for you. IIRC, this has been reported in the past.