Windows in the Overview don't have the close option if a popup is open
Mainly seems to affect Libadwaita applications, can't tell if anything else is affected, but things like GNOME Terminal don't have this issue. If the popups aren't considered a separate window, it probably affects those apps.
I don't believe any of my extensions are affecting this.
If I open a Libadwaita application and, say, open its About page, the Overview doesn't give me the option to close that application when I hover over its window.