To reproduce:
- Open the project and build the AssetBundles (Assets/Build AB)
- Open the Loader scene and change URLs on Loader script
- Press play. Everything works fine.
- Uncomment this line in Loader.cs: bundle.Unload(false);
- Press play and see that everything has been unloaded in the loaded scene.
- Change the call to bundle.Unload(true);
- Press play and see that everything has been unloaded in the loaded scene.

Reproducible: 5.5.0a1, 5.4.0b18, 5.3.5f1

Notes on why this is "Resolved (By Design)":

The root cause in this case is user called AssetBundle.Unload() right after SceneManager.LoadScene() without yield return null.

SceneManager.LoadScene() is not a real synchronous API, it only guarantee to be finished before next frame, users need to call yield return null after it.

Actually, we highly recommend users to use SceneManager.LoadSceneAsync().