Steps to reproduce:
1. Create new project
2. Create Cube prefab and script with public Object Test variable
3. Add script to a cube prefab (in Project window)
4. Create and set Sphere prefab as Test variable (in Hierarchy)
5. Save scene
6. Check scene dependencies left mouse button -> select Dependencies (2 objects 1 script 1 scene)
7. Remove from Cube script (in Hierarchy)
8. Save scene
9. Check dependencies (2 objects 1 script 1 scene)
10. Check cube prefab in the Project window. There isn't sphere object set as test variable. So it shouldn't be linked it as depended.

Expected results: 1 Cube prefab, 1 script and 1 scene is linked as depended
Actual results: 1 Cube prefab 1 sphere prefab, 1 script and 1 scene is linked as depended

Note: Reverting prefab unlikns Sphere from the scene

Reproduced with: 2018.1.0a7, 2017.3.0f1, 2017.2.0p4, 2017.1.2p3, 5.6.4p2