The duplicate error is usually caused by unnecessary files in your repository. In most cases, they were added manually by someone. It's important that the repository that SQL Source Control (SOC) uses doesn't contain anything else apart from files generated by SOC.
Make sure you are on the latest version.
To find the offending file, you can do a text search in your repository. If you have Notepad++ you can use the "Search > Find in Files" option to search the folder for instance of the string.
Once you find the issue, you'll need to delete it from the repository.
Finally, unlink and relink the database from SOC to refresh your working copies and transient copies.
If the problem persists please log a ticket with Support and attach a zipped copy of the Working Base and Transient Folders of the database where you are experiencing this issue.