Why do some sites have popups, even with software?

Mind giving some examples of said sites? And your version of FF? (So I can maybe try to replicate the problem.)

Uninstall Adblock and install uBlock Origin. It's faster and at least as effective. Once you install, choose your filters in the dashboard. See if there are any popup filters to choose from.

If that doesn't solve it, disable uBlock Origin, install uMatrix and uncheck all hosts files in the settings. uMatrix is what I use, but it's not for everyone because it requires some tinkering on the user's part (when not using hosts files, for first visits to some pages), which in turn requires learning how it works (which might be intimidating for some people). If you can't get rid of the popups by blocking some or all page elements with uMatrix, then I'd venture to guess you have malware.

Funny how everyone using adblock gets masses of popups.

Some the websites make in a certain way so adblock doesn't think it's an ad