Can anyone check Google Webmasters Tools to see how many unindexed posts/pages/categories they have? Things were pretty much going great, everything submitted was indexed, but in the last couple of days I started getting reports with lots of unindexed items. I checked everything I could check and found no reason why those shouldn't be indexed.
And then I just checked the WP SEO settings for the categories, and the setting "Include in sitemap?" was set to "Autodetect". I changed it to "Always include" and it immediately it appeared in the sitemap. It was always on autodetect and everything worked, but it seems that with recent updates something's changed.