How to reproduce:

1. Open attached project
2. Delete the AssetBundles folder from the root directory of the project
3. Go to menu AssetBundles -> Build AssetBundles From BuildMap
- Also make sure Simulate AssetBundles is unchecked for now
4. Open scene TestScenes/AssetLoader.unity
5. Play the scene
- Note the warnings: The referenced script on this Behaviour is missing!
- And the errors: GameObject (named <object name>) references runtime script in scene file. Fixing!
- Only Cube1 and Cube3 are referenced at this point (Cube2 is not referenced)
6. Stop and play scene again
- Cube1 appears to load properly (though the editor still throws errors)
- The loading gets as far as the "GameObject (named 'Cube2') references runtime script in scene file. Fixing!" error and then stops.
- Subsequent replays of the scene don't cause any changes in the error/warning patterns
- None of this happens if Simulate AssetBundles is checked in the AssetBundles menu (it is necessary to assign the cube prefabs to their respective AssetBundles)