Okay, that dot is the Dead Orbit icon. Apparently I had a Dead Orbit bond equipped which caused any bounties completed gave an increase to Dead Orbits reputation. The Dead Orbit is one of the three factions to choose from. Others are New Monarchy and Future War Cult
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I was having the very same problem, which is why I even saw your post. Check your equipped inventory. Somewhere there you will find item(s) associated with Dead Orbit. If you wear something from another faction, all bounty points will go to said faction. Simply unequipped the items, and you will start receiving Vanguard Rep.