I have the same issue, but when using 1 keyboard and the xdotool. I use
xdotool to input keypress like XF86AudioPlay, and others multimedia
keys. This only happen when using the gnome. In wayland there is no such
issue. The real keyboard does not have the multimedia keys. The system
became shortly unresponsive everytime I switch from the real keyboard to
the xdotool media keys, and vice versa.

This issue looks similar to this issue in Debian:
https://gitlab.gnome.org/GNOME/gnome-shell/issues/856

and I understand is has already been fixed with this patch, although I don't 
know how to use it :
https://gitlab.gnome.org/GNOME/mutter/merge_requests/579

** Bug watch added: gitlab.gnome.org/GNOME/gnome-shell/issues #856
   https://gitlab.gnome.org/GNOME/gnome-shell/issues/856

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https://bugs.launchpad.net/bugs/1777708

Title:
  Desktop briefly becomes unresponsive when typing on 2 keyboards at the
  same time

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