How to reproduce:
1. Open the attached project
2. Check AssetBundleBuilder.cs script and change BuildTarget platform to yours
3. Build AssetBundles (Assets -> Build AssetBundles)
4. Open and play Main scene
5. Check the console and notice warning "The referenced script on this Behaviour is missing!" and error "GameObject (named 'Test') references runtime script in scene file. Fixing!"

Additional note about user experience: We've also seen something similar happen in other projects where there's no error, but UnloadUnusedAssets unloads things that have just been loaded (in flight async load), and they get re-loaded synchronously when accessing them (e.g.AssetBundleRequest.asset) for the first time

Not reproducible: 5.3.3f1