I have a sitemap file that has been submitted to Google, and has been processed, according to Google Webmaster Tools.
As per GWT for 2013-05-31, 8255 web-pages are submitted, but only 8209 are indexed.
Which 46 of the 8255 pages are not indexed?
ThompsonPaul wrote on moz.com about figuring out which pages are not indexed. Here is a summary of what he has to say:
Clearly this is a manual and time consuming task that isn't going to work well if you site has more than thousands of pages.
Under the Google Webmaster Tools menu:
Health -> Index Status -> Advanced (tab)
Downloading the "Total Indexed" and comparing that against both the "Total Crawled" and the links in your sitemap should give you an idea of which were not indexed. You could use a file comparison application or spreadsheet to sort and organize the data accordingly.
I would suggest waiting a bit longer however as Google might still be crawling links outside your site or otherwise not finished.