To reproduce:
1. Create new project
2. Create cube and its prefab, delete cube from scene
3. Drag prefab to scene (do not release mouse button), when cube in scene will be visible, drag it to hierarchy (now MB can be released)
4. Actual vs Expected: There are 2 cubes in scene view and 1 in hierarchy instead of single cube in scene
5. Save and reload scene. 2nd cube with identical name appears in hierarchy
6. Drag prefab to scene and hold mouse key. Notice how it 'grows up'

Reproduced on: 2017.1.0b1
Not reproducible on: 5.5.3p1, 5.6.0p1, 2017.1.0a2

Regression introduced in 2017.1.0a5