Pi-hole is designed to block domains.
If an ad (or the javascript code used to generated the ad popup) is loaded from a blocked domain, Pi-hole will block it.
Popups are annoying, but seems that the popup in the screen shot is also an old article from the site. Either that or the screen capture missed the popup.
To be sure, there is other popups on the site that appeared while navigating through the articles on the site. Not not a great user experience experience, but also, as mentioned by rdwebdesign, there is little Pi-hole can do if the popup is served by the same site you are visiting, or another site that is not blocked.
I’d attribute this to bad script on the site that does no properly handle the user having already seen the popup.
For what it’s worth, a popup also appears on that site with UBlock Origin extension running in the web browser, which is pretty unusual. In this test, Pihole is not running.