Sure, but regardless of people doing dumb things, it's still worth asking "why did docker delete non-orphaned named volumes?" -- though you could also question whether someone was actually mistaken about them not being "orphaned" - you could probably arrange an unfortunate timing collision between someone running prune and a container being respawned.
Right, that's what raising an issue with the software maintainers are for.
Aside from anecdotes, there's little value in further discussion beyond the PSA that is the original post; save for prevention/recovery of such events.
It almost sounds as if the daemon was in the process of starting the containers and the prune command was issued. If it were run with `-f` and the container wasn't running those volumes would be deleted. I tried this on a test system and didn't get the results in the issue.