Why do I fail quests I haven't accepted or started?

It's because you have killed off what I'll call "objective markers" for future quests. What I mean is if there is a quest related to you interacting with a person, and you kill that person before the quest starts / you complete it, then you fail in that particular quest - regardless of whether you knew about it beforehand.

For Motor Runner there are a couple of different quests such as helping the NCR and a drug related quest for the Khans. The quests are as follows

Aba Daba Honeymoon

Bounty Killer (the one the OP was most probably doing)

Killing him off will fail the latter of the two in your case.