The best example that comes to mind is mouse acceleration. Fedora has a setting in the GUI for it but it didn't work. So I literally had to set it in my bashrc to get it to work.
Another issue I saw was os theme being multiple settings depending on gtk or qt apps.
Another issue is video card driver. I've had Ubuntu auto update and brick my install, dropping me down to grub because grub was set to use my Nvidia proprietary drivers but the kernel module wasn't installed despite me setting it in the GUI to use the Nvidia drivers.
Multiple issues with peripherals and having to install a random GitHub Python script for watcom drivers or Xbox controllers.
Oh, also vpn settings on the os level didn't work on debian recently. I had to configure it via command line.