On one of my (many) systems, I found that the theming was “different” from the others. Some flatpak applications looked broken, e.g. light-themed menu on dark-themed system, inconsistent fonts, and so on. After looking further, I noticed the Platform libraries (org.kde.Platform and org.gnome.Platform). After installing them, the the applications in question look normal.
So I suggest checking with flatpak list to see if you’re missing them.