How to reproduce:
1. Create a new project
2. In the Hierarchy create an empty Game Object
3. Drag it to the Project window to make it a prefab
4. Right-click the prefab and select show in explorer
5. Copy the GameObject.prefab.meta file to another folder
6. Select the Prefab and create a new AssetBundle for it
7. Exit Unity
8. Copy the GameObject.prefab.meta file from another folder to the Assets folder
9. Launch the project again and select the Game Object prefab

Expected result: Game Object is not in an Asset Bundle
Actual result: Game Object is in an Asset Bundle

Reproducible with 5.6.6f2, 2017.4.20f2, 2018.3.6f1, 2019.1.0b3, 2019.2.0a5

Fixed in: 2018.4.2f1, 2019.1.5f1, 2019.2.0a12, 2019.3.0a2