Ran into an issue where a Nintex site workflow was running and appeared to get stuck. The workflow status via the “View Workflow History” link was displaying as Completed, but the workflow still seemed to be running. So, I needed to cancel the site workflow.
To terminate a site workflow:
- Verify that you have the following administrative credentials: You must be a member of the Site Owners SharePoint group on the site that you are configuring.
- Browse to the home page of the site for which you want to terminate a site workflow.
- In the Quick Launch, click View All Site Content and then click Site Workflows link at the top of the page.
- On the Workflows page, click the name of the workflow that you want to cancel in the My Running Workflows section.
- On the Workflow Status page in the Workflow Information section, click “Terminate this workflow now”.
- In the dialog box that appears, click OK.
TechRhodes 
Great article on terminating workflows interactively! We actually just posted an article on how to terminate workflows through a Nintex workflow. Check it out.