Hello,

When you make a list template of a list that contains workflows, the workflows get carried over but they are invisible to the Nintex designer. I like to refer to these as "ghost flows".   The good news is you didn't do anything wrong.

Thanks

Mike

See if this solution works for you as well:  

I like solutions, don't you? I ran into this exact issue but found no solutions here even though this is a very old post. I did find out how to solve it. So I would like to share. 

I can reproduce this issue two ways. 

1. On a list with a Nintex Form and a Nintex Workflow I create a list template. Then I recreate the list some where else in SharePoint using the list template.

2. Or, I use Content Matrix to copy the list to another site somewhere else in SharePoint. 

The Nintex Form always transfers very nicely with the list. All you have to do on the new list is edit the Nintex Form and then publish it and you are all set. But the Nintex workflow is an entirely different story. When you click on Workflow Settings Manage Workflows with Nintex Workflows you have no workflows listed. But when you create an item in the new list it somehow magically runs the workflow from the original list. 

So what is happening here is that it is copying the reference to the workflow along with the list. When you create a record it is running that reference to the original workflow. You just need to delete the reference. How? Go to Workflow Settings and click on Workflow Settings...the first item on the drop down menu. You will see that it has a reference to the original workflow. Just click on "Remove, Block or Restore a Workflow". Then you can select "Remove" beside the workflow and OK to delete the reference. 

Thank you all for this thread, and thank @ rangelin for the solution.
I had the same problem: I created a copy of List, I checked that I don't see any copied workflows. Then a colleague has created an Item in this copied List and the WF from original List was run! And it has sent some emails!! Not good.

In my opinion this is a bug. Either Nintex should not copy the WF with the List or (preferably) it should copy the WF, but then the WF should be visible in the copied list. This is not a good sign of Nintex that this issue still exists after 4 years. @nintex - do something with it!.