I would start with the Controls in Use pane and review all of the layouts. If you have linked controls from one layout to another this should not be an issue. Maybe a link was removed?
I was getting this issue with a form that had a desktop and a mobile version. Both forms shared the same control name, like first, last address etc. I had to go to one of the forms and rename the controls to first1 last1 address1. then Nintex was happy. I opened up a ticket with Nintex to see why this behavior is occurring at this time. When the initial forms were created in February, Nintex did not issue any such warnings, so we were able to publish them both layouts.