As far as I can tell there is absolutely no way to tell your city has been hit with a debuff other than to go into each attribute and check the details. IE if the AI casts Antipathy on your city you need to open the city window, hover over unrest, find a line that says "Antipathy 10%" and then remember that Antipathy is a city debuff spell.

There used to be something more obvious in the city details windows, I don't know when it was removed, I'm assuming this was a bug. In either case it wasn't enough back then and now it's just ridiculous. City debuffs should show on the city frame on the world map, like below the build progress bar mirroring the essence buff circles.