I have experienced this same scenario on mixed US / AA itineraries several times. One case involved a couple of very long international flights where they were refusing to give me mileage credit for the flights. They let me on the return trip without much argument, but put their feet in the ground on the mileage credit and refused to budge.

Since it was a refundable ticket, I disputed my credit card charge and told the credit card company that the airline was stating I didn't fly the flight and since it was a refundable ticket they also were refusing a refund.

This forced US / AA to figure out the issue and provide proof I flew the flights, which was then the same proof used to provide me the mileage.

It was way more effort then we should have to go through, but, it did appear to me as it was multiple computer systems not exchanging information correctly.