/etc/init.d/mongod

Here is the line from parse PIDFILEPATH

PIDFILEPATH=`awk -F'[:=]' -v IGNORECASE=1 '/^[[:blank:]]*(processManagement\.)?pidfilepath[[:blank:]]*[:=][[:blank:]]*/{print $2}' "$CONFIGFILE" | tr -d "[:blank:]\"'"`

The default configure file come from rpm /etc/mongod.conf for pid is

  pidFilePath: /var/run/mongodb/mongod.pid  # location of pidfile

When daemon parse PIDFILEPATH from configure file, it get the comment line too.

Now the issue is
pid file be created by mongo using the configure/option file, which support "#".
Daemon use PIDFILEPATH parse trying to get some pid file to find pid and kill. It got incorrect file name and cannot kill mongod for clean shutdown.

What user saw is using standard systemctl stop mongod.service or service stop mongod, prompt will return OK but cannot stop mongod.,