1. What happened
If you have a Physics joint referencing another GameObject in the same scene, and then move the GameObject to a separate scene and enter play mode, a duplicate game object is created in the first scene. This is not restored to the previous state after leaving play mode.

2. How we can reproduce it using the example you attached
- Load scenes '2' and e.g. 'Ground1' (if not loaded)
- Select 'DoorBlock' GO
- In its 'Hinge Joint'>'Connected body' select a rigid-body GO from the same scene (e.g. Sphere)
- Move 'Sphere' GO to another scene (e.g. Ground1)
- Enter Play mode
---> Notice that 'Sphere' GO is created in scene '2'
- Exit Play mode
---> 'Sphere' GO now exists in both scenes.
Expected: GO should not be duplicated. Likely the best thing would be to remove reference to GO the moment it is moved to another scene. Might be worthwhile informing user in console about the action (smth like 'Reference to ... was removed because ...').

Same behaviour in 5.3.0f4.