Steps to repro:

1. Open Unity;
2. Open attached project;
3. Go to Assets -> Scenes;
4. Open 'Main' scene;
5. Open Build Settings;
6. Add open scene by clicking "Add Open scene"';
7. Build the scene for Standalone platform (either Windows or OSX).

Actual result:
3 same assertion messages appear in the console:

'Assertion failed on expression: 'asset->mainRepresentation.type == TypeOf<GameObject>()'
UnityEditor.HostView:OnGUI()'

See attached actual.png screenshot.

Regression introduced in Unity 5.5.

Expected result:
Assertions should not appear after building project.

Notes:
- Reproducible in 5.6.0a1, 5.5.0b11;
- Reproducible on both OSX 10.12.1 and Windows 10;
- Not reproducible in 5.4.2p3;
- Not reproducible in new project/bug seems to be project-specific.