Quest Targets respawning. Bosses disappearing

[Fennrick]

Two things that feel kind of strange:

1. Even after having fully completed a hunting quest, the target ships/creatures keep reappearing in that sector. So for Example sector 27 will always have a space phoenix in it and sector 13 crawls with unfriendly "gruff troublemakers" even after i killed them and turned the quest in. Is this working as intended?

2. Exploring my second temple i encountered some evil and quite deadly space creature. So i did the logical thing and ran away.
Now after a few hours of playtime and getting stronger equipment i revisited the temple and fully explored it. The aforementioned monster was nowhere to be found. Just gone.

Are these bugs or all part of the greater plan?

edit: The "Trap Achievement" does not seem to work. It still shows 0 activated traps and i ran into many traps already.