1. Open Plasma NM
2. Turn off WiFi
3. Click on the resulting notification's close button

..and what do you think should happen?

Given the close button on the notification popup has focus (from hover), it should close only the notification popup or at least close it first.
The systray popup closes immediately after it looses focus, so clicking the notification popup actually makes the systray popup loose focus, then it animates any maaaybee kwin puts it over the notification, so your click actually ends up in the systray popup (wild guessing here however).

This is just a symptom of a more general problem: That notifications appear at the same place as the systray popup.

We could solve this either by positioning the notifications elsewhere. Personally I'd like to put them on the top-right corner by default, but allow users to move them wherever they want them. If the user clicks the notifications icon in the systray, however, they should of course still be shown in the sytray popup.

What about moving the popups out of the way when the systray popup is opened? Ie. they move up by whatever height the systray popups size is? Don't know if/how that is possible.