Is our sub-domain messing up our seo for our root?

[opusbyseo]

We have a website (mysite.com) that we control and a subdomain (affiliate.mysite.com) that is 3rd-Party Content completely out of our control. I've found that nearly all or our Crawl Errors are coming from this subdomain. Same deal with 95% of our warnings: they all come from the subdomain.

The two website are very much interlinked, as the subdomain serves up the header and footer of the root domain through iFrames and the 3rd-party content in the middle-section. On the root domain there are countless links pointing at this 3rd-party subdomain.

How do these errors affect the root domain, and how do you propose we address the issue?

[HandsomeWeb]

The common thought is search engines consider the sub domain as an entirely different website, but your sub domain may be your competition.  If you are selling yellow widgets on example.com and you are selling widgets on affiliate.widgets.com, you are competing against yourself.

Many of the errors and warning you are getting may be affecting just the affiliate.example.com.

If you site at affiliate.mysite.com, search engines probably recognize the content in the iframe as belonging to the Affiliate Company's website.

I believe you can do the diagnostics here for separate sub domains.  That may help your focus on your controllable content.