Here is what I think happened. The agent saw that it was booked in A class which for AA means both discounted revenue first and upgraded first using miles. Given that most upgrades within the US are on 2 class services they may have mistakenly believed that it was an upgrade from coach. Something similar happened to me on a oneworld circle pacific ticket issued in A class. Taking my flight from NRT to SJC the agent asked me if I still wanted the upgrade and if so she would deduct the miles from my account. I suggested she look a bit further into the booking and note that it was an actual revenue booking in A class not an upgrade - a few keystrokes later and she was satisified.

Nevertheless, this does not excuse AA's actions. It is appalling that airport staff are not adequately trained in the difference between revenue and non-revenue classes. Though why AA chooses the one code to mean more than one thing is beyond me.