Even if not in the same PNR, an AA agent can find the CX e-ticket.

That is not the issue here. The suggestion was that someone at AA proactively went looking through the records of other tickets and placed notes in them. That is simply not going to happen.

It is more than likely that CX looked at the PNR and placed the note so that its own agent would collect the fee.

Bear in mind that if a fee was due from the passenger and CX failed to collect it, AA would still get paid. It is CX which would have been out the money. AA simply has no reason to concern itself with whether the passenger has paid CX.