Looking at the user project, the references in the scene file is of type "MonoScript". MonoScripts tends to be serialized into a scene file for:
- Special case MonoBehaviours, authored by Unity, with a native backing (e.g. Entity’s SubScene)
- Script references from Unity 4.x and older
We couldn't figure out how these references ended up in the scene file in the first place, but the assembly name points towards that these were somehow created by the user.
The GameObjectUtility.RemoveMonoBehavioursWithMissingScript-API is created to remove MonoBehaviours from GameObjects which are missing their script file. Since the GameObject has a MonoScript, not a MonoBehaviour, the API is not suitable for this type of action.
If we find out how these MonoScript references were added to the scene file, do file a new bug report, so that we can take a closer look at it with updated repro steps.