I was having the same issue also.
I could not understand why I am getting Faces on my iPhone 5 when I have not checked any people in the Faces section of the Sync Dialogue Box.
I found another discussion that has a reasonable explanation:
It explains that any photo you have chosen to import to your phone that has a Face already identified will automatically be sorted by Faces ALSO, meaning in addition being put into the seclected Album you may have chosen and also identifies and sorts your chosen Photos by Faces.
You will notice if you look at a particular Faces Album that not all of the Faces of that person are on the phone, only that Person's Face from your imported phone photos.
I think you would find it is not duplicating the photo twice, but it is just being additionally identified in the Faces section
I hope I have not confused you more.