I have to admit that this isn’t a new issue in Unity 6.1, it’s been a longstanding problem that generates quite a bit of noise in version control and all the related headaches. It needs some attention again imo.
The issue is that the sorting of the m_Modifications array in prefabs doesn’t seem to be stable. Without any manual changes, the array elements sometimes get shuffled around, which then shows up in version control as modifications. Even when you commit files that Unity has automatically changed, they may reappear later with the m_Modifications elements reordered by Unity again.
Is this issue on your radar? I haven’t submitted a bug report yet because it occurs randomly and these kinds of random issues rarely pass QA.
