We renewed our website last year (2012) in December. After that we have put 301 redirection in place for the required pages. We removed some pages in old site when we moved to new site.
For example : In the old site we had
http://www.mydomain.com/article/ and in new website we removed it.
Pages that don't exist in new site we redirect it to 404 page. Since then, the
Webmaster -> Crawler Errors -> Not Found report shows these old URLs with a Response code of 404. Also the Linked from section displays internal site links that refer to this page. When I checked these pages, the link is not found.
I understand by reading this Google link http://support.google.com/webmasters/bin/answer.py?hl=en&answer=2409439 that these error don't harm our SEO, but I would like to know the exact reason why these happening.