@Srivatsan - I've seen a number of these sorts of posts about the duplicates... and here is my hypotheiss of what occured..
the taxpayer filled out the tax return and submitted it. No duplicates were apprarent on the screen or on the copy of the tax return that the taxpayer print / placed in a *PDF.
But the data that transmitted to the IRS created these duplicates, which obviously were not apparent or evident to the taxpayer looking at the computer screen or PDF file.
One would assume and trust that the transmitted file is an EXACT reflection of what the taxpayer sees on the screen or is documented to the saved PDF file... But what if that wasn't true?
Can you actually see the duplicate in your PDF file?
