All passengers in a single PNR must be on the same flights and in the same cabin. Changing even one flight of one passenger, or upgrading one passenger, "breaks" the PNR. And once you are on separate PNRs, even if it was the result of a momentary mistake by an agent, there is no way to put you back together without cancelling everything and creating an entirely new booking.

Fortunately AA does not (yet) change seat assignments if separating PNRs makes one of the pax ineligible for their current seat. Some other airlines do exactly that.