This happened to my sister when she and I were traveling together. We both had our account numbers on our respective reservations. We completed our first segment and I was checking us in for the return portion. I noticed her reservation had my OnePass number on it. Neither of us had done anything that would have resulted in the change. The only thing that was done between the time we had checked in for the outbound segment and the time we checked in for the return portion was request that she get on the upgrade standby list as a companion.
This caused her not to get mileage for the outbound portion. I changed her reservation so that it had her OnePass number and she did end up getting mileage for the return portion. She had to request for the outbound portion to be credited and it took about a month. Like many have already mentioned, be sure that the name on the reservation and the OnePass account match.