google ranks URLs, not files on a web server.
I suggest you 301 all your index.html files to the corresponding directory URL.
see [webmasterworld.com ] and scroll down to canonical issues.
Google indexes URLs, not "pages" - and you have two different URLs that display the same content. You have noticed what is called a canonical URL problem - and it is a sign that the actual content for that page is havong it's tota; Page Rank "split".
The key is to let Google (and the other search engines, too) know that there is just one preferred canonical URL for that content, no matter which version the spider used to find it.
One very good way to do this is to use a 301 redirect from /services/index.htnl to /services/
Another way is to use the rel="canonical" link tag in the head of this content.
my idea was that google reaching my www.domain.com, was aware that was reading the index.html or index.php, therefore samething.
So you're saying that google can show, in a search result, the same page twice for that search, if they had the same rank, one following the other, is that it?
yes, Google can show the same content twice in a search result if they've indexed it with two different URLs - although they try to filter out all but one URL.
The big deal with canonical URL problems is that your possible total page rank is being split, and no one version of the page is getting all the ranking power that it might have. There are mnay other forms of canonical URL problems - "with-www" and "without-www", or http: and https:, or with and without a query string for example.
Taking on the technical responsibility for these potential splits in PageRank can help to improve search traffic in some cases by accumulating all your backlink power under one "canonical" URL.
Other discussions about canonical URL issues can be found in the Hot Topics area [webmasterworld.com], which is always pinned to the top of this forum's index page.:
Merging www.example.com/ and www.example.com/index.htm [webmasterworld.com]
Why Does Google Treat "www" & "no-www" As Different? [webmasterworld.com]
Removing https pages from Google with robots.txt [webmasterworld.com]
Canonical URL Issues - including some new ones [webmasterworld.com]
This issue is now much clear to me.
Duplicate pages carrying different pageranks shows how unimportant pagerank actually is, you can't rank 2 identical pages in search.
What about domain.com/index.htm?
On one site we only have content on index.html but WMT says there are several links to index.htm, which is very puzzling since we have always used .html there. Should I 301 .htm?
If there are backlinks pointing to index.html, then I would definitely set a 301 to index.htm so you get the ranking power of those links.