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I have a sub domain that isn't even on our own site but it's resulting in a lot of errors in Moz for duplicate content, as shown here: http://cl.ly/1R081v0K0e2N. Would this affect our ranking or is it simply just errors within Moz? What measures could I take to make sure that Moz or Google doesn't associate our site with these errors? Would I have to noindex in the htaccess file for the sub domain?

I just started doing an SEO audit and noticed I have 40,000 some odd back links from an OLD version of our site that has been moved to a subdomain. The back links are for articles that already exist on our main site. I don't think Google is picking it up as duplicate content because that site isn't being crawled anymore. Could this hurt us SEO wise? I plan on removing the site, but how long after it's been removed should those back links disappear?