Sometimes when shutting down a VM via the standard XenCenter interface or command line (xe) on a Citrix XenServer machine the shutdown will not complete.  The first thing to try is a force shutdown on the VM:

xe vm-shutdown –force vm=[vm name]

If this still doesn’t work you can try taking a look in the XenServer pending task queue:

xe task-list

And cancel the process’ that seem to be holding up the system:

xe task-cancel uuid=[task uuid]

If this still fails you can try the following:

xe-toolstack-restart