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)

I don't remember exactly, but I think Apache was started via systemd because there was no error like "Apache is not started". Systemd was reporting that it is stopping and starting Apache but in fact it did nothing.