My experience is that if they had that much trouble posting the miles, giving them back will be even more difficult for them. Only exception was that massive Goldpoints extra transfer a couple years back; they seemed to have fixed that on their own even though many of us advised them of the error. Also the extra Hilton points from that auto site quickly disappeared on their own.
I recently TWICE advised an airline they had only deducted the 80000 miles for my husband's ticket and none for mine; the second CSR actually said, "I won't tell anyone if you won't." It was obviously too much trouble for him to fix.