Just to clarify further about non-respawning enemies, the ones that do not respawn are attached to a generated structure like a ruin, dungeon entrance or dungeon interior.

For example the burial chambers in black forests typically generate with a small arrangement of skeletons guarding the entrance. If you kill these ones they will never come back. It can be a bit difficult to notice this right away because enemies that spawn like this are indistinguishable from their randomly roaming equivalents in every other way.