Sometimes VMs stuck in an unresponsive state and once you give shutdown command via XenCenter VM never goes offline. The first step could be to do toolstack restart so that you can try force shutdown command. If this is also not resolving the issue you need to find the dom id of the VM and kill it from the command line.
Below are the steps:
1. Go to general tab of the VM and copy the UUID
2. and then on the XenServer console, run the following to get the domid
list_domains | grep UUID
The first column is the dom-id of the VM.
3. Run the following cmd to destroy:
/opt/xensource/debug/xenops destroy_domain –domid idoftheVM