Jujutsu: a new, Git-compatible version control system

I don't know what keys/commands you are using to get the behavior you see, but I'm using bog-standard Magit with all the basic settings and very little customization. The key I use to unstage a hunk is "u". If the cursor is on a hunk that's been staged, then the hunk is moved back to "unstaged changes" by pressing that key. If the cursor is on a hunk in a commit (I view the hunks in the commits by selecting a commit in my "Recent Commits" list then pressing ENTER to see its changes) then I get the behavior I described previously.

Perhaps you are entering some other "commit editing mode" in Magit, that I'm not using. It sounds cool! But in any case there is a clear difference in the UI behavior between staged hunks and hunks in commits.