I've had issues with Filezilla on both z17 & z18 wayland on 2 separate machines with theme colours resulting in black text on black background, invisible heading column dividers and re-draw issues in file browser. The last of which was most problematic as files & folders would 'disappear' until you'd selected each one which made it quite unsafe to work.
I had these issue both with the apt & flatpak distributions.
Anyway, I finally found a solution to both issues so I'll share it here. Instructions are for the apt distribution, but should work similarly for flatpak, you'd just need to figure out the executable (I can never remember how to launch flatpaks from terminal!) & paths:
Launch filezilla from terminal with:
GTK_THEME=Adwaita-dark GDK_BACKEND=x11 filezilla
If you prefer the light theme just set it to Adwaita
If that works and you want to make the change permanent, copy the .desktop:
cp /usr/share/applications/filezilla.desktop ~/.local/share/applications/filezilla.desktop
Then edit the copied filezilla.desktop and change the Exec= line to:
Exec=env GTK_THEME=Adwaita-dark GDK_BACKEND=x11 filezilla
Then save & refresh the desktop database:
update-desktop-database ~/.local/share/applications/
All sorted!
Maybe one day filezilla will get GTK4 support. I'll not hold my breath.