OP, the issue caused is NOT your fault. You arrived on time (actually much earlier) and had to deal with incompetent agents who did not know what to do, leading to the delay in waiting for a 'supervisor' to handle the issue. I blame this solely on AA for not being able to solve the issue in a timely manner, leading to a bunch of BS that should have never happened in the first place.
In regards to flyingeph12's responses, WHY should the customer be liable for the fact that AA can't get their .... together when it comes to upgrades on a split PNR? Should everyone know split PNR upgrades often run into issues? Why should anyone know about split PNR upgrades causing issues? This should be addressed to AA agents on how to deal with the issue and NOT for the customer to do research and understand.