I use "GNOME on Xorgs", today I have try to update f38 to f39.
Like occur on F38, also into f39 some apps, like Firefox or Libreoffice, have top bar size different from gnome native apps like gnome-terminal or nautilus.
Also the Middle-Click mouse button set to "lower" click on top bar do not work on the apps with different top bar
You can try this problem also use the last F39 Workstation live version (Fedora-Workstation-Live-x86_64-39-20230907.n.0.iso), if you set password to liveuser then logoff and logon with "GNOME on Xorgs" you can see this problem.
If you use default GNOME on Wayland, lower function work on all top bar type
I have also fill this bug: https://bugzilla.redhat.com/show_bug.cgi?id=2192180
See also
In GNOME 44, window top bar doesn't work properly under Xorg https://www.reddit.com/r/gnome/comments/12ubuya/in_gnome_44_window_top_bar_d...
There is a workaround to resolve this annoying issue?
Many thanks
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Dario Lesca