I have recently been informed that the only Bounty Hunting kills counted on the PvP kill counter are when you are factional and hunting someone of the oppostie faction for a bounty regardless of Special Forces status. As such I see this behavior to be a bug that needs correcting: Bounty Hunting kills should not be counted on PvP kills on the grounds that the PvP kill counter is inherently linked to your GCW faction, rank, and GCW points generated.
To prevent further confusion I would even ask that the counter be renamed to GCW PvP Kills and only count kills in combat in which both parties are Special Forces before combat is initiated between the two parties. However, this would admittedly be rather low priority. I would prefer the dev's time be spent working on areas of the game in need of more attention such as the weapon enhancements, addressing the mustafar weapons, and spending time just ironing out some of the small stuff where they can. That said, I will be sure to add this to my agenda to ensure it does not slip through the cracks.