Prefabs not working correctly

Hi,

I've recently run into a problem that's pretty annoying concerning prefabs (which means that yes, I could go around it by doing everything manually and I'll probably do that for now, but it's time consuming for nothing), and I was wondering if anyone else encountered this, or has any advice. Whenever I add a new component to a prefab asset, when going back to the scene, this new component will be "disabled" (not available and marked as "Removed"). I also tried adding the component to an instance of the prefab asset and applying the change to the prefab via the menu after right clicking, but that crashes Unity (happened twice so far, I sent a bug report).

Could it be something I'm doing that's making Unity angry, something I might not know about this new prefab system?

Screenshots for clarity.