Most links to my site are to from VPS nameserver?

[gotwithit]

I have a VPS (let's say: vpsexample.com)
I have two websites running on the VPS (www.site1.com) and (www.site2.com)

The name servers are: ns1.vpsexample.com and ns2.vpsexample.com

I have Google analytics for both sites. Site 1 seems to be ok and has a good even distribution of incoming links (20 links from site a, 15 from site b, 10 from site c, etc.) Site 2 has weird behavior in analytics, specifically for "links to my site".

In analytics, I have over 2,000 links to my site2 from my VPS domain. If my content's URL is: www.site2.com/content1, google lists it as ns1.vpsexample.com/content1 and if I click on it (ns1.vpsexample.com/content1), it takes me to what appears to be Site 2, except the URL in the browser is ns1.vpsexample.com/content1

I went into my VPS control panel, checked the DNS settings for Site1 and Site2 but they seemed to be OK (meaning I looked over them and they were the same in regard to nameservers.) What is wrong? Sorry if I didn't explain this well!

[storminternet]

Check your website and nameserver entry in webserver configuration and confirm if both are not using same location to keep their files or folders. For example check virtualhost entry of your website and nameserver if you are on linux/apache webserver.

[alemcherry]

I guess this is some sort of test URL which Google indexed by mistake. Once a single URL is indexed, all other pages are crawled from the page and since the links are relative, they are added under same domain.

What you can do now it to have an .htaccess set up to redirect all ns.vpsserver.com/something to correspoding URLs with correct domain name. They should be set up as 301 redirect, to make sure that ranking is not lost.