To know the exact number of links indexed for your site never rely on GWT, it often updates slowly and reporting partial results if your site was existent in past years. The number of indexed links reported for the sitemap in this case is the amount of new links added to the Google index contained in that sitemap. GWT does tend to fluctuate/change every so often, so use it as a general reporting tool.

Technically only for just new sites the number of links in the sitemap may be equal to the reported number of indexed links in GWT.

If your site has been online for example since some months and you submit a sitemap using GWT, the number of links reported as indexed will be only the difference between links already available in the Google index and links available now thanks to the newly submitted sitemap.

Moreover Google has complex algorithms that are able to discard certain duplicated contents (called internal duplication), so if your links are considered as pointing to duplicated contents they could be discarded from indexing. Even links considered as not selected as canonical, duplicated pages without canonical, alternate pages without canonical and pages with redirect are discarded.

To know the real total amount of your site links added to the Google index, execute the search site:www.mysite.com in the Google search. This will show all the real pages indexed for your site and the whole list. You will get also all links contained in the sitemap that are already included in the Google index.

In the following case of an existent site the number of indexed links is the difference of newly added links thanks to the sitemap.

In the following case of a new site the number of indexed links is equal to the number of links submitted.

In some other cases links used for sitemap generation could be not refreshed immediately by Google Webmasters Tools/Search Console that could use a caching system. To ensure to force GWT to refresh and fetch a new copy of your sitemap you can submit an alternative link for example activating the SEF version of sitemap links. As a result the link will be rewitten from http://mysite.com/index.php? option=com_jmap&view=sitemap&format=xml to http://mysite.com/component/jmap/sitemap/xml

Another way to force Google Webmasters Tools/Search Console to refresh sitemap stats, is adding an extra parameter to the link submitted. If the standard sitemap link is: http://mysite.com/index.php? option=com_jmap&view=sitemap&format=xml you can activate the parameter 'Enable random links for sitemaps' to add an extra parameter 'ver=1234' and submit again the new link: http://mysite.com/index.php? option=com_jmap&view=sitemap&format=xml&ver=1234

As a final check ensure that your robots.txt, the htaccess or server firewalls are not preventing Google to index your site. More info about this issue and stats issues of Google Webmasters Tools/Search Console at this address: https://productforums.google.com/forum/#!topic/webmasters/vVrwkHUzhT0