You may choose the creature you put the -1/-1 counter on to get another -1/-1 counter when proliferating.

The state-based action that removes matching +1/+1 and -1/-1 counters won’t check until after you proliferate and Grim Affliction finishes resolving. It’s possible to remove up to two +1/+1 counters from the creature by choosing to put a second -1/-1 counter on the creature when proliferating.