I've ran into this issue many times with the nexus and archon priest. I can't say that I did any damage to the boss in the final 30 seconds but that shouldn't screw me out of the bounty if I'm doing crowd control during that time.
Are you doing damage to the strike target within 30 seconds of it going down? Are you near your teammates? If you do not do any damage to the boss towards the end, the bounty may not get marked as complete. https://www.bungie.net/en/Help/Article/12187 I've also had a few instances where I or a fireteam member didn't get credit, even though they were doing damage, but we were all spread out. It seems like you have to be somewhat close to the guardian that lands the killing blow too.