Drupal duplicate alias for same node
That might be because of Locale core module. I had the same problem, but when i disabled the Locale module the problem was gone. 

You can observe the main cause of the problem. When you look into the duplicate url aliases you will find the difference between the original url alias and duplicate url alias. In the original url alias you will have language = " and whereas with new/duplicate url alias you will find language = 'en'. 

Hope this answers your question.