Webmaster tools under Crawl errors shows mydomain.com/index.html as a 404 error and that it has been linked from 100 pages there are 2 things that are wrong with that. - I haven't had index.html but index.php almost from the start. So it has been index.php for at least 3 months now. Being index.html for just few days or so in the very beginning of the site. - Those 100 pages that are supposed to be linking to mydomain.com/index.html are actually linking to just mydomain.com/ So where this index.html comes from?
Sometime the weird links are come from content scraped blog. You can got them fixed by done 301 redirect from one version to the one you are preferring. This Guide could help you get the job done.
If that link do not exist or has been removed, then you can submit URL removal request from Google webmaster tool. You can also submit to remove complete directory.