When using the Update Document action, content within Rich Text fields are duplicated.
Upgrade to the latest build of Nintex Workflow. More for information on this process, see Updating Nintex for SharePoint - What you need to know.
This was a known bug within Nintex Workflow for SharePoint. This has been fixed in build 126.96.36.199 for Workflow 2013, and build 188.8.131.52 for Workflow 2010.