Martin - On many sites, it's natural that the inner pages rank better than the homepage. It depends, of course, on the query.
In this case, what's unusual about the situation that causes you to ask about it?
Is the ranking for a query where you had expected the homepage to be ranking higher? OR, is it simply on a site:example.com search, where the homepage "traditionally" is expected to be listed first... but in your case it isn't?