Occasionally this happens. I wound up bokking a flight to MSY later this month on Orbitz, because I couldn't pull up the same fare on AA. Usually I'll put a decent effort into pulling the fare up on AA just so I can use the discount and get the booking bonus.
But every now and then, I can't find it.

One thing that bothers me about AA.com (and maybe I'm imagining it) - if I search by schedule, a lot of the time it pulls up the exact same flights as the "fare" search, but at a higher price. And sometimes, if I've been searching by schedule, I swear it keeps offerring me only much higher prices than are available when I search by fare again.
What I WANT is for the website to give me the lowest fare available for a given selected schedule. If they want to offer me the option of flying in a higher fare class, that's fine, give me little check boxes so I can pick the fare class I want (YUP when other are paying, discount when I am).