I just went through a very similar situation but finally got it sorted out. On a two-leg flight my AS number was only credited to the first leg and the second went to AA. I had to initially call into AA to get my AS MP# on the tix so not sure why they'd think that was what I wanted. I'm guessing it was just an oversight by AA. Anyway, I called AS and was told to call AA to have the miles removed from that account (fwiw, calling into AA was a total nightmare - can't believe that's a functioning airline). AS said take screenshots of my AA account before and after the miles were removed, then send that into the AS mileage plan email. Did that and received an email a couple days later saying thanks, miles have been credited... except they weren't. So, I kept replying to the email (with a case#) and was totally ignored. I replied three times with no reply from AS. I finally called in yesterday and the lady on the phone was ultra-apologetic and even gave me some extra miles. She apologized up and down that they ignored my three emails.

The good news - I got a live person on the phone at the AS MP within a couple minutes both times I called.