I run 2 sites, Site A and Site B. These are ecommerce sites, with site A being built first, and both sites selling the same thing. They are hosted separately, use separate CMS (one magento and one pinnacle), and do not use duplicated content. We sell chemicals, this is important because we make available for download (by law mind you) the Labels and MSDS's for said chemicals. These are legal documents that are written by the manufacturers for the consumer's safety, etc. My problem is that my GWMT account shows over 16k backlinks going from site B to site A, and all 16k can be associated with 24 pdf files on site A that were simply copy and pasted into site b's server. GWMT shows them as backlinks "via intermediate" links which should indicate both a link somewhere AND a redirect somewhere, neither of which exist. There are no links, there are no redirects anywhere in my code. These should not be showing up in the first place. I have no unnatural link flag warnings. Is anyone having this issue, or have a solution for this issue? Why is google showing these as links in the first place? Am i being penalized for duplicate content?
Google is certainly recognizing the duplicate content. unless you are seeing ranking drops, it is unlikely that you are being penalized. What happens is likely:
While you have a legal obligation to publish this content and make it available to your users, you don't have to make it crawlable. There are several reasons that you might want to block it in robots.txt:
For more information, you should read What is duplicate content and how can I avoid being penalized for it on my site? about when Google does and does not penalize for duplicate content.