You should call and talk to them, escalate to a supervisor if need be. I once had a situation where I was materially misled by a phone agent, I explained what I had been told, when I'd called before, etc., and it was all fixed up while I waited on hold for a while.

(My situation was that I had booked a roundtrip ticket and called to pay the difference to upgrade my outbound flight to F, I paid the difference -- but it turned out that the agent replaced my roundtrip with a ticket for only a one-way outbound in F, even though my online reservation appeared to remain intact. I traveled outbound but was unable to check in for the return and was told I'd changed & canceled it and the return would now be $600 or whatnot, and they fixed it all up. Now, my small part of contributory negligence, perhaps analogous to yours in failing to read the fare rules, was that when I paid the difference in fare, I [though I had no real way to know] paid only the difference between my purchased rt Y ticket and a one-way F, removing the cost of the return Y leg, which was not too much at the time it was bought, but which was still something. But that didn't matter -- AA made it right.)

Good luck.