When you click on Team and then commit, files in the workspace which should not be checked will always appear in the list of files to commit. You can mark a file to be ignored. This will prevent it from being put into the commit list. This is not a temporary action. It can be undone and should only be used on files that will never be checked in but often exist in the workspace. To indicate that a file should be ignored, right click on the file then select Team and then Ignore. In this example a test.dat file is marked to be ignored in commits.