Steps to repro:

1. Open attached project and t1 scene;
2. Launch the scene.

Actual result:
DontDestroyOnLoad scene appears in the Hierarchy view. See attached video.
Regression introduced in Unity 5.6.0f1 and 2017.1.0a3

Expected result:
No additional scenes should appear in the Hierarchy after launchning the scene, unless some object(s) in this scene are marked as DontDestroyOnLoad.

Notes:
- Reproducible in 2017.1.0a4, 2017.1.0a3, 5.6.0f1;
- Not reproducible in 5.6.0b11, 5.6.0b10, 5.5.2p1;
- Reproducible on both OSX 10.12.3 and Windows 10;
- Reproducible only in the scene with painted trees, not reproducible in a scene with dragged tree prefabs or with primitive gameobjects (cubes).