She said she called ahead of time to both arrange the dogs and wheelchair request.
At this stage, I think we can conclude there was a change of airplane, some combination of special requests, and possibly lack of status which knocked her out of first class. And just some poor gate management on AA's part which upgraded two others over her paid ticket.
Last mystery: Some people had mentioned that it is possible due to the aircraft change that the two others upgraded over these folks may also have been paid first as well. Would the upgrade list on the board list people who were paid first, seated in economy, then placed back in first as an "upgrade"?
If they were correctly denoted as DSR, then yes, they would show up on the board for upgrades above any other passengers (listed by status).
So it is definitely possible that the 2 upgrades were F pax downgraded and got the seats due to being higher status than the other passengers.