Agreed - "non stop" flights with a stop always count as one segment, or one mileage posting. If you had booked it outright, then I doubt you would have any recourse. I still think you may not have any recourse because you volunteered to go standby, (if it was an oversold situation, equipment problem, etc it would be different).

Nevertheless, a sincere plea to customer service that it was an unintentional oversight may do the trick. It has worked for me in the past with involuntary re-routes. The call is free....