Steps to reproduce this issue:

1. Open the attached project
2.Build AssetBundles (AssetBundles->Build AssetBundles from the menu)
3. Load the "Main" scene.
4. Press Play
5. Observe the errors logged ("GameObject ("name") references runtime script in scene file. Fixing!")

This also results in strange errors where MonoBehaviour fields that are initialized in Start() are null in Update() despite never being set anywhere but Start(). See the "How did testObject become null?" error appear in the console after entering playmode