empty Gameobjects persisting even in a new Scene

This is a weird one to me, but I’m sure it’s probably just something about the editor that I don’t get.

So basically, I created some basic prefabs, with a floor cube, some more parented cubes etc. and I wanted to add some empty gameobjects to the prefab, that’s fine, I did that, but after I delete the prefab from the scene the empty gameobjects stay in the scene. They’re not in the Hierarchy, but because they’re visible with icons, I can click on them. What’s most strange (at least from my point of view) is that when I create a new scene, these 2 gameobjects are still there!!! They’re somehow linked back to the ones in the prefab.

here’s a screencast of what I’m talking about:

If anybody can help I’d very much appreciate it. It’s probably something I’ve done very wrong but so far I’ve never come across something like this as the Editor is so uber-intuitive !

Thanks

Try downloading the newest version of Unity, as it seems like a known bug they fixed in 3.4.1:

Quote from the release notes:
“Icons on newly created Prefabs no longer stay after the Prefab is deleted from the scene.”