After some firm words with the agent (Cantonese line), they said they will reverse it.

I told them that the outbound flight HKG-KIX did not have my MPC# and miles were not credited. I asked them how come my inbound flight KIX-HKG got credited, when I specifically asked not to credit it and the boarding pass showed no MPC#.

They said if the number was present when I made the booking, it can still show up in the system even after manual removal.

I told them that this was not acceptable and they need to remove it for me.

After holding the line for a few times, they said they will get the department concerned to remove it.