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Categories sometimes not saved in database
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On Swedish Wikipedia [[sv:Special:UncategorizedPages]] fills up with bot created new pages. These pages have categories in the wikicode when created, but for some reason the categorylinks are not stored in the database. This makes the categories appear at the bottom of pages, but the pages are missing in the category pages.

The problem has existed at least since the beginning of the year with som new pages appearing on each update of [[Special:UncategorizedPages]]. Only very few (probably much less than 1%) of the pages created by this bot have the problem.

It is easy to fix the categorisation with null edits, manually or by bot. But that does not fix the cause of the problem.

Event Timeline

Opening one of these pages for editing I also see that no templates are listed below the edit area.
And following a link from the page and looking at [[Special:Whatlinkshere]] the link from the page is missing.
So neither templatelinks nor pagelinks are stored in the datebase.