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?