This looks similar (the same?) as How to prevent Magit from saving COMMIT_EDITMSG? but I've also confirmed that the problem isn't magit itself, but interactions with settings or other packages.
I'm having the same issue as 46965 (though it just started recently) -- my second commit goes to the previous git commit and bypasses the options for commits.
I am definitely using
C-c C-c to commit and I see the commit in the log.
I tried running a bare magit using the info in the debug section of the manual -- that instance worked as it's supposed to (goes to the options). So it sounds like either settings or other packages are causing the problem. I turned off all other magit packages (magit-section, magit-todos, vdiff-magit) but the problem is still there.
Has anyone else seen this behaviour and found out what the offending setting/package is?
My setup: Magit 20200228.1207, Git 2.25.1, Emacs 28.0.50, gnu/linux