During the development of Caelium Alpha (using Unity), I was trying to fix weird bug in which trying to spawn 1 planet actually spawns multiple planets. I was not able to fix the bug by the time the LD Jam ended, which was obviously concerning. Now I wake up the next morning to fix the problem, and I found out that a prefab (for planets, stars, etc.) that references itself was being set to a gameObject, even though I never asked for that.

Long story short, if you have a prefab with a script that references that very same prefab itself, the prefab will turn into a cloned gameObject. Very annoying "bug", but unfortunately Unity says in the forums that it was intentionally designed. I still don't understand how, but the moral of the story is:

Don't let a prefab reference itself. It can jeopardize your development time (like it did for me).