Pluggable authentication modules are the core of user authentication in any modern linux distribution. Modules pam_passwdqc and pam_ecryptfs were removed between CentOS 6 and CentOS 7, thus making some PAM configuration files no longer valid. Preupgrade assistant will comment out these modules in your PAM configuration files after the in-place upgrade automatically, but you should review and regain the authentication functionality other way, if these modules were required for your authentication policy.