Why are only some of my scripts missing/"failed to load" only when loading the prefab from a bundle?

When instantiating prefabs loaded from asset bundles, some of their script components give the "referenced script is missing" / "associated script can not be loaded" error and some do not. I can't find any significant difference in the failure cases. So, I'm looking for insight on how this is expected to work.

The bundles contain a single prefab each and are built using (abbreviated):

 BuildAssetBundle(AssetDatabase.LoadAssetAtPath("foo.prefab"), CollectDependencies)

The prefabs are loaded using (abbreviated):

 WWW www = WWW.LoadFromCacheOrDownload(url, version);
 AssetBundle bundle = www.assetBundle;
 www.Dispose();
 AssetBundleRequest request = bundle.LoadAssetWithSubAssetsAsync("foo.prefab");
 yield return request;
 GameObject go = request.asset as GameObject;
 bundle.Unload(false);
 GameObject foo = GameObject.Instantiate(go);

Note that if I comment out "bundle.Unload(false)" everything works fine. But, with the Unload in place, certain scripts fail during instantiation. I am certain that the bundles are not out of sync because I'm rebuilding them during my tests. The scripts are all compiled into my app. I would expect "GameObject go" to hold a reference to the script that survives the Unload. Indeed, that does seem true for some scripts, but not others. I have not identified the difference between the two cases.

Is this expected to work or am I misunderstanding? This is with Unity 5 Beta 22, btw.