In a tweet, Google’s John Mueller said that it was okay to list a URL twice in a disavow links file:
@Photogkris @mattcutts Duplicates don't cause problems (but make your maintenance harder). I sort text-files before submitting— John Mueller (@JohnMu) 30. Oktober 2014
If you want to find bad backlinks that can hurt the rankings of your website, use the link disinfection tool in SEOprofiler.