Pay attention when adding prefabs to AssetBundles if they contain references to ScriptableObjects. Since ScriptableObjects are essentially assets, Unity creates duplicates of them before adding them to AssetBundles, which may result in undesired behaviour during runtime.
When you load such a GameObject from an AssetBundle, it may be necessary to reinject the ScriptableObject assets to the loaded scripts, replacing the bundled ones. See Dependency Injection