If the PDF is a preprint it should not get matched to a pubmed paper that was published (not a preprint)
If the PDF is not a preprint it should not get matched to a pubmed-index preprint.
If a paper was published and its preprint was also indexed by pubmed, there may be a link in the pubmed XML.
I'm not sure if its possible for a paper to have been published, and for its preprint to have been indexed in pubmed, but for the published paper to not have been indexed in pubmed.