This is one of the most annoying aspects of frequent flier programs. I have had all sorts of trouble with United -- I have had mileage flown on Star partners occassionally not credit, and mileage flown on other partners (namely, Qatar and Emirates) not credit even more frequently (the majority of the time, in fact). And my Mileage Plus number was associated with the reservation, printed on the boarding pass, etc. One of the flights was even a single PNR -- DXB-LHR-IAD -- and the Emirates segment didn't credit. And United is very slow in fixing it (I sent them a letter, with boarding passes and receipts, two months ago, and they still haven't even acknowledged receiving it, much less credited the miles).

With American, one flight each on OneWorld partners Iberia and BA posted; several segments on non-OneWorld partner Turkish have not. Strangely, I have never had a problem on Northwest, although I have had fewer cases and rarely with a non-SkyTeam partner. You should be able to get yours fixed more easily because US is part of Star Alliance, so AC should have an easier time verifying the flights.

I think that the airlines deliberately don't try very hard in an attempt to squeeze a few miles out of customers.