How to reproduce:
1. Open attached project
2. Select New Prefab(1) and in Inspector apply prefab changes
3. Select New Prefab(2) and in Inspector apply prefab changes
4. Undo these changes
5. Observe console

Errors:
Component of type MeshRenderer was added to New Prefab (1) using GameObject.AddComponent() and had become dangling during an undo operation.
Use Undo.AddComponent to correctly add a component which can be handle by the undo system

System is already interested in this transform, SetSystemInterested may only be called once.

If the system is getting enabled, then it can't have any previous changes registered

System is not interested in this transform, SetSystemInterested may only be called on transforms that are set interested.

Reproduced with: 2021.2.0b8, 2022.1.0a6
Unable to test on 2021.1.18f1