The duplicate error is usually caused by unnecessary files in your repository which have resulted in duplicate CREATE statements for an object. In most cases, the files were added manually to the repository. It's important that the repository that SQL Source Control (SOC) uses doesn't contain anything else apart from files generated by SOC.
First make sure you are on the latest version of SQL Source Control (Help>Check for updates).
If the error remains: to find the offending file, you can search your repository for all the CREATE statements for the object referenced in the error. If you have Notepad++ you can use the "Search > Find in Files" option to search the folder for instances of the CREATE string or object name.
Once you find the issue, you'll need to delete the duplicate CREATE statement from the repository and commit.
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.