OP, I'm eager to hear why you think AA should then boot the two passengers out of biz they upgraded per their own rules, to get you back on well after booking, well after check-in? I mean to be honest, this is how this would be. "Hey mr or mrs, I have to return you back to coach again, and unfortunately since I gave your seats away all that is left is middle seats. So sorry that we took them back and then screwed you over by giving you worse seats than you had to begin with despite the fact you were here on time. I had two people who were just re-booked onto this flight well after booking and check-in was done.
So AA's choice was to punish the people who were there on time per the rules. They would then either have to move more people around to get them their seats back, or worse tell them they are now super-screwed and have awful seats. OR tell the people who they just last minute rebooked onto the flt technically against their own rules, that they are sorry but they can get them on but not together. Keep in mind the people who rebooked you onto it likely weren't even involved in the gate for that flt, so that means someone else re-booked you late onto someone else's full flt.
I'm sorry but seeing the bigger picture, AA did exactly what they should have here.