This is probably explained best with an example. In the Commons category https://commons.wikimedia.org/wiki/Category:17th-century_portrait_paintings_of_men_not_categorised_by_year, the first subcategory "17th-century portrait paintings of men, artist, location and year missing" is displayed as containing 2 subcategories, with an activated arrow button for the subcategory drop-down list. But this subcategory doesn't actually contain any subcategories.
There are various similar examples other categories, such as https://commons.wikimedia.org/wiki/Category:Hidden_categories, e.g., 1 Chome Higashikaiganminami in Chigasaki from panoramio
This problem doesn't seem to occur in Wikipedia.