Definitely a glitch. If they aren't helpful, write back that they didn't have an accurate number of souls on board for that flight, and suggest that you will write a DOT complaint, that will get it escalated.
Update:
I submitted a complaint on AA's website, and got the automated reply letter initially. A few hours later, a member of the Customer Success team emailed me and apologized for what happened. The email said they were going to escalate the matter to Customer Experience and Technical Support for further investigation. This afternoon, I got a call from AA. Another member from the Customer Success team reached out to discuss what happened. The rep said he was a senior rep and has been with AA for 26 years. In his entire time, he has never seen this situation happen. He even conferred with another senior rep from the team, and neither could make sense of why I was removed from the flight and not on the manifest. He also said it was wise of me to
save the boarding pass as a screenshot (main takeaway point for those who don't do this), because if I pulled up the BP in the app, this would have not worked after my reservation was split from my companion and deleted. They were going to further escalate this internally, but whatever their findings are could not be shared with me. Ultimately, he stated the LPs, million miles, and award miles would be corrected and posted to my account. They posted within the hour. Finally, he gave me an additional 5K miles for everything that happened.
All in all, a positive result from AA imo. It would be nice to find out what ultimately happened, if they are able to interview the gate agent that made all the changes. But it is what it is.