Doing a black sacrament today and the bonus objective was to kill Lucky, the neutral kagouti.
I did this first, it registered as complete and I went on to kill the main target. As I approached the exit with plenty of time to spare and no alerts, my journal updated and I saw text saying that the bonus objective had failed, confused, I ran back to the first area and saw that Lucky had respawned.
Killing Lucky again did not help as the quest entry had already registered as failed.