Do all the flights show correctly when looking at AA.com using your main record locator? If so, there is nothing to be concerned about.

AA uses Sabre, and will create a ghost PNR (or multiple) for your Amadeus flights which may only show a subset of flights relevant to those operating carriers (QR and BA). Opening these PNR's may therefore only show partial information and BA's avios/TP estimates wont be correct.