[AssetBundle] When loading prefab from asset bundle "GameObject references runtime script in scene file. Fixing" error is thrown
There is still a problem in 5.5.1f1 as far as I can tell.
If a script is referenced from a prefab, and the script (class) is renamed but it keeps the same GUID, then the prefab stays unchanged, and the AssetFileHash is unchanged, but the asset bundle file itself is different!
Since the AssetFileHash is unchanged, if you've already cached the previous asset bundle, LoadFromCacheOrDownload does not download the new bundle, and you get errors such as "The referenced script on this Behaviour is missing!".
But you don't see this error if you haven't already cached the previous version, so it's easy to miss until final production & test.