PB5: Leaving ProBuilder keeps making edits to many of my prefabs

It seems like this started with PB 5.0.1, as I don’t recall it happening in the 5.0-preview versions, but it’s possible I just didn’t notice.

Maybe once a day or so, on leaving Play mode in the edit, I see a bunch of errors telling me that assets can’t be destroyed. I then look at my pending changes, and I see that a bunch of prefabs contain changes, generally prefabs for which there were instances in the scene I just stopped. They mostly contain changes to the m_VersionIndex value of a PB component on the prefab:

I don’t have any steps to reproduce this, since it happens intermittently. But are you aware of any reason why leaving Play Mode would cause PB to modify the actual prefab assets in my project?

This happened again, so I got the actual console error:

Destroying assets is not permitted to avoid data loss.
If you really want to remove an asset use DestroyImmediate (theObject, true);
UnityEditor.Build.BuildPipelineInterfaces:OnSceneProcess (UnityEngine.SceneManagement.Scene,UnityEditor.Build.Reporting.BuildReport)

At this point, I don’t know if something else is responsible for the error, and ProBuilder is doing something weird in response to it. Or if ProBuilder is responsible for the error.