I've been playing for 2 years and continue to find this bug at random intervals. It will effect bounties, as well as the weekly count towards pinnacle gear in crucible and gambit.
Bounties and weeklies will just stop giving me credit. For example: I'll be in a strike, needing 150 Scorn kills. I check the bounty, I need 15 more kills. I kill 7 more, bounty has not counted any kill, or maybe just 1. Just yesterday playing Crucible Control - a friend and I played 4 matches, didn't get the pinnacle. Check my progress, says I only played 2 matches. We play 2 more matches. Now Crucible says I completed 3 matches.
Its incredibly frustrating, and usually the only way to fix it is to restart the entire game, and sometimes it is still a problem.
If you were trying to get the scorn kills in the final boss room of Hollowed Lair, then those enemies do not count for any bounty or quest. This is to prevent farming.
As for the crucible issues, there have been some reports stating the same, but playing more games resolved the issue for those users.