I see the same thing with Optiplex 9020 and BIOS A10.  For reference,
git commit 01414f897d20874f6f5d7ef2f756f5bf2df526fc introduced the
problem.

commit 01414f897d20874f6f5d7ef2f756f5bf2df526fc
Author: Denis Turischev <[email protected]>
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 <[email protected]>
    Reported-by: Wulf Richartz <[email protected]>
    Cc: Mathias Nyman <[email protected]>
    Signed-off-by: Greg Kroah-Hartman <[email protected]>
    Signed-off-by: Kamal Mostafa <[email protected]>

diff --git a/drivers/usb/host/xhci-pci.c b/drivers/usb/host/xhci-pci.c
index 3fc8d9e..21223f8 100644
--- a/drivers/usb/host/xhci-pci.c
+++ b/drivers/usb/host/xhci-pci.c
@@ -138,7 +138,9 @@ static void xhci_pci_quirks(struct device *dev, struct 
xhci_hcd *xhci)
                 */
                if (pdev->subsystem_vendor == PCI_VENDOR_ID_HP)
                        xhci->quirks |= XHCI_SPURIOUS_WAKEUP;
-
+       }
+       if (pdev->vendor == PCI_VENDOR_ID_INTEL &&
+               pdev->device == PCI_DEVICE_ID_INTEL_LYNXPOINT_LP_XHCI) {
                xhci->quirks |= XHCI_SPURIOUS_REBOOT;
        }
        if (pdev->vendor == PCI_VENDOR_ID_ETRON &&

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https://bugs.launchpad.net/bugs/1457852

Title:
  Optiplex 9020 reboots rather than shutting down if USB3 enabled

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