I am going to guess you did not start the apache via systemd? This is actually a feature: systemd only manages processes it has started. So if you started apache via /etc/init.d, you should restart it via /etc/init.d as well.

(note that the opposite is not true: many /etc/init.d scripts stop process by killing everything with this process name -- no matter if it is the right process, or user-specific one, or one managed by some other supervisor)