Flashing the recent BIOS update (FBKTA5A released 2015-01-06) resolved the 
problem for me:
http://support.lenovo.com/downloads/ds035753
Shutdown works now with kernel 3.13.0-44.

As I did a bisect from 3.13.0-43 to 3.13.0-44 before I did the BIOS
update here's the result anyway:

01414f897d20874f6f5d7ef2f756f5bf2df526fc is the first bad commit
commit 01414f897d20874f6f5d7ef2f756f5bf2df526fc
Author: Denis Turischev <denis.turisc...@compulab.co.il>
Date:   Tue May 20 14:00:42 2014 +0300

    xhci: Switch only Intel Lynx Point-LP ports to EHCI on shutdown.
    
    BugLink: http://bugs.launchpad.net/bugs/1402853
    
    commit 0a939993bff117d3657108ca13b011fc0378aedb upstream.
    
    Patch "xhci: Switch Intel Lynx Point ports to EHCI on shutdown."
    commit c09ec25d3684cad74d851c0f028a495999591279 is not fully correct
    
    It switches both Lynx Point and Lynx Point-LP ports to EHCI on shutdown.
    On some Lynx Point machines it causes spurious interrupt,
    which wake the system: bugzilla.kernel.org/show_bug.cgi?id=76291
    
    On Lynx Point-LP on the contrary switching ports to EHCI seems to be
    necessary to fix these spurious interrupts.
    
    Signed-off-by: Denis Turischev <de...@compulab.co.il>
    Reported-by: Wulf Richartz <wulf.richa...@gmail.com>
    Cc: Mathias Nyman <mathias.ny...@linux.intel.com>
    Signed-off-by: Greg Kroah-Hartman <gre...@linuxfoundation.org>
    Signed-off-by: Kamal Mostafa <ka...@canonical.com>

:040000 040000 2017c75e797dd6fde9e00f73db85fa32eeb19775
7d11924d8262e57dab18920cf19ec4c14e93db5f M      drivers

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https://bugs.launchpad.net/bugs/1320282

Title:
  [Lenovo ThinkCentre M93p] reboots instead of shutting down

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