To reproduce:
1. Open attached project.
2. Open "main" scene.
3. Take "cloud 1" sprite and drag it into scene and then back to the project window. (It gets stuck in the scene view)
4. Press Play. (Now stuck sprite is saved in the scene without a gameObject)

Expected result: If object was not placed in the scene - it does not stay in the scene.
Actual result: When object is moved from the scene view, it gets stuck on a border inside the Scene view.

Reproducible: 2017.1.0a4
Not reproducible: 5.6.0f1, 2017.1.0a3

Notes:
Works with sprites and prefabs.