Autorenew vhost ambiguity

I do have files in /etc/httpd/conf.d, and yes they are loaded by apache. My apache install is whatever is the latest by yum from base or epel for CentOS 7. I’ve also installed some php stuff like phpAdmin if that matters. Should I send these to you as well? Is my WSGI vhost causing the problem?

[lking@loutilities httpd]$ pwd
/etc/httpd
[lking@loutilities httpd]$ grep IncludeOptional conf/httpd.conf
IncludeOptional conf.d/*.conf
IncludeOptional sites-enabled/*.conf
[lking@loutilities httpd]$ ls conf.d
autoindex.conf  fcgid.conf  php.conf  phpMyAdmin.conf  README  ssl.conf  userdir.conf  welcome.conf
[lking@loutilities httpd]$ grep VirtualHost conf.d/*
conf.d/ssl.conf:<VirtualHost _default_:443>
conf.d/ssl.conf:</VirtualHost>
[lking@loutilities httpd]$ grep -ir -e servername -e serveralias conf.d/*
conf.d/ssl.conf:#ServerName www.example.com:443

[lking@loutilities httpd]$ yum repolist
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: centos.mirror.nac.net
 * epel: fedora-epel.mirrors.tds.net
 * extras: mirror.symnds.com
 * updates: mirror.us.leaseweb.net
repo id                                                 repo name                                                             status
!base/7/x86_64                                          CentOS-7 - Base                                                        9,363
!epel/x86_64                                            Extra Packages for Enterprise Linux 7 - x86_64                        11,479
!erlang-solutions/7/x86_64                              Centos 7 - x86_64 - Erlang Solutions                                     779
!extras/7/x86_64                                        CentOS-7 - Extras                                                        311
!rabbitmq_rabbitmq-server/x86_64                        rabbitmq_rabbitmq-server                                                  12
!rabbitmq_rabbitmq-server-source                        rabbitmq_rabbitmq-server-source                                            0
!updates/7/x86_64                                       CentOS-7 - Updates                                                     1,126
repolist: 23,070

[lking@loutilities httpd]$ yum list installed | grep httpd
httpd.x86_64                    2.4.6-45.el7.centos            @base
httpd-tools.x86_64              2.4.6-45.el7.centos            @base
[lking@loutilities httpd]$ yum list installed | grep apache
python2-certbot-apache.noarch   0.12.0-1.el7                   @epel

[lking@loutilities httpd]$ yum list installed | grep php
php.x86_64                      5.4.16-42.el7                  @base
php-bcmath.x86_64               5.4.16-42.el7                  @base
php-cli.x86_64                  5.4.16-42.el7                  @base
php-common.x86_64               5.4.16-42.el7                  @base
php-fedora-autoloader.noarch    0.2.1-2.el7                    @epel
php-gd.x86_64                   5.4.16-42.el7                  @base
php-mbstring.x86_64             5.4.16-42.el7                  @base
php-mysql.x86_64                5.4.16-42.el7                  @base
php-pdo.x86_64                  5.4.16-42.el7                  @base
php-php-gettext.noarch          1.0.12-1.el7                   @epel
php-process.x86_64              5.4.16-42.el7                  @base
php-tcpdf.noarch                6.2.13-1.el7                   @epel
php-tcpdf-dejavu-sans-fonts.noarch
php-tidy.x86_64                 5.4.16-7.el7                   @epel
php-xml.x86_64                  5.4.16-42.el7                  @base
phpMyAdmin.noarch               4.4.15.10-1.el7                @epel