For the implementation of `mouse-autoselect-window', the entered window
is remembered and then compared when an mouse motion event is received.
Up to Emacs 28, this value was stored in a static local variable named
`last_mouse_window' in the block handling MotionNotify within
`handle_one_xevent'.  With the introduction of XInput 2,
`handle_one_xevent' was adjusted to account for XI_Motion events, with
the oversight that a new local static `last_mouse_window' variable was
declared in the new handler block for XI_Motion.  As a result, when
Emacs receives motion events from XInput and XInput2 sources
alternatively the value of each `last_mouse_window’ differs, leading to
the window under the motion sometimes not being selected, as the
value `last_mouse_window' is out-of-date for the particular XInput
version.

This bug impacts the GNU ELPA package EXWM.  EXWM tries to extrapolate
applicable Emacs functionality to X window management; among others
assigns an Emacs buffer to each managed X window, and positions the X
window over the Emacs window in which the buffer is displayed.  When
`mouse-autoselect-windows’ and the user moves the mouse pointer over one
X window managed by EXWM, this X window receives the mouse events and not
Emacs, therefore the Emacs window is not selected.  In order to overcome
this, EXWM sends a synthetic MotionNotify event to Emacs.

The attached patch fixes the issue.

Thank you,
Adrián Medraño Calvo.