Three days before this report in ptwiki we added a category to a template that are in many pages, but those pages still don't appear in the category list. All pages show the category in the footer, but only one of them is listed in the category members list.

The edit that added the category: https://pt.wikipedia.org/w/index.php?title=Predefini%C3%A7%C3%A3o:Cab-ice&diff=62567834&oldid=56983028
The pages (of category namespace) that transclude the template and should be in category list: https://pt.wikipedia.org/w/index.php?title=Especial:P%C3%A1ginas_afluentes/Template:Cab-ice&hidelinks=1
The category list where the pages should appear: https://pt.wikipedia.org/w/index.php?title=Categoria:!Categorias_vazias_que_n%C3%A3o_devem_ser_eliminadas&subcatfrom=I (<-note the subcatfrom=I)
Image of that category list linked above in the time of this report (3 days after the category was added to the template): https://phabricator.wikimedia.org/F34881231

I checked the job queue one day after in the siteinfo API, and it said '"jobs": 0', so I don't think that is because a big job queue, and I think a big job queue doesn't dalay 3 days to complete.
I also checked the category members in the database with quarry: https://quarry.wmcloud.org/query/60617

Why is that category list important? We are thinking in use a bot to delete empty categories with some exceptions, the members of that category is one of the exceptions, so if a category page that should be categorized in that category is not, that can make a category page be deleted when it should not be. And I can image other maintenance tasks can also have some problem when that kind of bug happens.