After migrating source control successfully, you should verify that the sources have been migrated to Team Foundation source control. After a successful migration, you should see whether there are differences between the latest versions of files and folders in Visual SourceSafe to the latest versions of the migrated sources in Team Foundation source control using any file comparison utility such as the WinDiff tool. If you find differences between the files, folders or their versions, you should migrate the latest version manually. This mean you have to add some files manually which are not present in Team Foundation and delete the ones which are not present in VSS. Some of these problems are due to VSS corruption issues, some are due to scenarios which cannot be taken care off by converter and Team Foundation issues.
You always find some extra files on the Visual SourceSafe side with the extension *.*scc. These files are temporary files generated by Visual SourceSafe in your local folder when you use a get command for the latest in Visual SourceSafe . The extra files are not source files.