If a linux system user is able to login on the shell or with SSH depends on its shell setting in /etc/passwd. If you want to prevent that a certain user is able to login, then set the shell either to /bin/false or /sbin/nologin.
Example for Debian and Ubuntu Linux for the user with the username "otheruser":
usermod -s /bin/false otheruser
For Redhat, Fedora or CentOS use /sbin/nologin:
usermod -s /sbin/nologin otheruser
Warning: Do not set the shell for the root user to /bin/false or /sbin/nologin!