This bug does not seem to be GNOME specific since the problem happens in
usermod. Maybe KDE does not use usermod.

Have you tried running the usermod commandline from a fresh boot, i.e.
before you tried to edit the user with users-admin? Maybe that's the
program that is locking /etc/passwd (via the backends).

As lslk did not return anything, could you try 'fuser /etc/passwd' too?

-- 
usermod fails: "cannot lock /etc/passwd"
https://bugs.launchpad.net/bugs/432964
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