I have a similar discrepancy in my account. It might have been a flight from Europe which got changed due to irregular ops. When I returned, I requested the difference in miles from my original itinerary (LHR-MIA, MIA-EWR), in addition to the ones I received for the flight I had been changed to (LHR-EWR). After I noticed the discrepancy, I called AA. They won't fix it, but they assured me that the actual total is the higher one.