Hi there. Thanks for your response.
The pages exist on the new site, but the subdomain should have never been indexed. I noticed the back links in Google Console initially then confirmed with SEO Power Suite.
Basically we had site.com, then created a brand new site and migrated content over to newsite.com with 301 redirects from the old site. Then we wanted to keep the old site up for reference so we put it at admin.site.com. That is where all the 40,000 back links were coming from, admin.site.com, the old site.
There is no reason for us to redirect admin.site.com since the original articles were properly redirected. I guess however some how when the old site was taken down, Google must have indexed it still at the subdomain and counted those as backlinks.