This section was not there before latest update (4-6 weeks of code) of translatewiki.net.
I suspect it is caused by rSTIMb46734465699: Timeless: support SidebarBeforeOutput hook. It looks like that an extension on translatewiki.net defines afterPortlet content for the languages section, but there are no languages to render, and Timeless doesn't actually show the afterPortlet content, resulting in an empty portlet. CC'ing @Ammarpad as author.
I can see that here https://translatewiki.net/wiki/FAQ?useskin=timeless.
It does not happen with other skins so I believe the problems lies with Timeless handling of the portlet header (not content). Because if it were content, I'd expect monobook https://translatewiki.net/wiki/FAQ?useskin=monobook (or vector) to show the content, but they don't, as there's none.