How to reproduce:

1. Open an X11 terminal emulator, for example xterm
2. Run emacsclient -e '(completing-read "Prompt: " (list "1" "2" "3"))'
3. Select something from the list
4. Try to type something into the X11 terminal.

The first keypress after the minibuffer is closed seems to go to the underlying emacs buffer of the EXWM window instead of to the X11 window inside it, causing a "Buffer is read only" error. Subsequent keypresses after the first one is sent correctly to the X11 window.

EDIT: Note that this only happens if the minibuffer is opened by other means than through a keybind. If I open the minibuffer by pressing M-x, 'C-x b' or similar, then the focus is returned correctly to the X11 window.