It's possible it was reticketed on AA prime codes rather than the original BA codeshares, If something is resolved manually it's easier for the agent to do that, and in which case the only downside if actually flying AA metal is that may give slightly fewer Avios than the codeshare version.

So if AA.com and the AA app is all looking good for you, then that's fine. If there is only AA prime codes used then it will probably be an entirely SABRE booking, and therefore no dummy Amadeus PNR created (no need) and therefore it won't be picked up in the BA app or BA.com. But there is not particular problem with that, in a way one less thing to go wrong.