Operating system: elementaryOS 0.4.1
Graphics card: GTX 1080
Broken: 2.80, 964b5f02caf8
Short description of error
When duplicating a scene by clicking "Link Object Data" it's not just the object data that becomes linked, but the object itself is somehow linked. There is apparently no way to make these objects single user objects anymore, not even by clicking on the little "2" next to object name in properties panel.
Exact steps for others to reproduce the error
Open attached file and try to make the cube a single user.
Or open default blender, click on duplicate scene with Link Object Data and look at user and behavior of "Cube".