Comment by helterskelter

From Archwiki:

Godot runs on Wayland using Xwayland, which causes a variety of UI issues, when not running in single window mode. [1] To get around this, start Godot with godot --single-window, then open a project, and enable single window mode in the editor settings.

This issue has been resolved in Godot 4.1.1. [2] This issue seems to have recurred in Godot 4.2 [3]

With Godot 4.3, Wayland can be used natively. [4] There are two ways to do this:

    Set the command-line argument --display-driver wayland.
    Enable the editor setting located at run/platforms/linuxbsd/prefer_wayland.

The above only makes Godot's client to run under native Wayland, but games still run under Xwayland. In order for games to run under native Wayland, go to project settings, click on "Display Server" at the sidebar, and at the option "Driver.linuxbsd" select wayland.

https://wiki.archlinux.org/title/Godot_Engine