What is called Canonical Issues in search engine?

Canonical Issues take place when a search engine treats www.yourdomain.com, yourdomain.com, and yourdomain.com/index.html as different web sites. When Google does this, it flags the different copies as second copy content, and penalizes them. If yourdomain.com is not penalized and all other web sites link to your web site using www.yourdomain.com, after that the version left in the index will have no ranking. These are basic issues that other major search engines, like Yahoo and MSN, have no problem dealing with. Google's reputation as the world's utmost search engine (self-ranked as a ten on a scale of one to ten) is hindered by its incapability to resolve basic indexing issues.