If you can log in using ssh with that user, you should be able to kill off the other sessions on the machine. The trick is to identify them.
command will show information which should be helpful including the PID of the login shell. You can check what that session is "doing" using
You should be able to kill off session which have been left idle from your ssh session, assuming it's the same user.
I'm assuming you're logging into a machine using bash as the shell (do "echo $SHELL" to find out ). If so, you can edit the user's .bashrc file (or the global /etc/profile if you want the change to be applied to all users), adding the line
which will make the shell auto-logout if left idle for two minutes (120 seconds).
You might want to use a timeouot larger than this - it's annoying for users to get auto-logged out frequently. Maybe set it to an hour (3600).