I AUPed on a recent itinerary which was a slightly fiddly one with BA and AA sectors in it, despite being one booking it had weird ticketing and nested PNR disconnects that meant I couldn't check-in online for half the flights, or kept losing my seat assignments on the AA metal. One sector in particular kept going "unticketed", even though it was. Wasn't a Oneworld "superior, seamless travel experience" by any stretch.
However the Avios and TPs for the AUPed sector automatically credited correctly without any intervention.