A couple of questions to help start troubleshooting… Is it only flatpaks? Can you confirm “Appearance” in “Settings” is set to “Dark?” If you have GNOME Tweaks installed, is the “Legacy Applications” setting correct for your theme?
Okay… You could try copying the flatpak’s .desktop file to your ~/.local/share/applications/ folder and make some changes to it to try and force the theme; that is, cp the “bottles” .desktop file in /var/lib/flatpak/app/[bottles directory]/current/active/files/share/applications/ to ~/.local/share/applications/, open it with an editor, and add env GTK_THEME="Sweet-Dark"after the Exec= and before the executable.
That could/should/might work… If that’s unclear, let me know the name of the bottles directory in /var/lib/flatpak/app/ and I can try to be more specific.
My guess is this can be attributed to the “un-theming” forced by the new libadwaita stuff; i.e., user themes was always jury-rigged to work and recent changes to GNOME make it work with far less reliability.