How to reproduce:
1. Create a new Unity project
2. Create a new Prefab and add any Component to that Prefab
3. Create a Script and attach it to the prefab
4. Drag the Prefab onto the Scene to create a GameObject
5. Remove the attached Script Component from the GameObject
6. Right-click the Script in the Project window and select "Find References In Scene"

Expected result: the GameObject created from the Prefab does not show up as a reference
Actual result: the GameObject created from the Prefab is still listed as a reference, despite no longer having the Script associated with it

Reproducible with: 2017.1.5f1, 2017.2.3p2, 2017.4.8f1, 2018.1.9f1, 2018.2.1f1, 2018.3.0a6

Notes:
Reproduces with any Asset, that can be attached to a Component
Does not reproduce when after deleting the referenced Component the only Component left on the GameObject is 'Transform'