Packaging Prefabs Cleanly (no objects outside etc)

Hi All,
I recently followed a tutorial, that showed

1. creating an empty prefab
2. dragging components into it
3. clicking on prefab and selecting dependencies
4. exporting prefab as package.

My challenge is that when I open the prefab, many elements are outside the package, and it gets hard to keep everything organized (ie. I'm trying to make multiple rooms, then import 10 rooms as prefabs into a new clean project).

Can anyone offer a good tutorial or advice on the way to package a prefab cleanly?

ie see in attached image, I open the prefab and everything is there, nothing is nested and can't 'close' the nesting order.