Can you help with this mystery? Old website's hyperlinks linked to new website.

[farm gate]

The site owner wanted to start over and did the following to create a new site
-Used the Google URL removal tool to remove the old site from the index.
-Used Robots.txt on the old site to disallow search engines
-When the old site was gone from the index, placed the new site online. The new site has a different home page than the old but the inner pages are all the same.

A couple of weeks later, according to WMT the new site suddenly had 10,000+ links that previously had pointed at the old site's home page. There is a line underneath each link saying "Via this intermediate link: [old site]"