I stumbled upon that as well, but it requires a closer look because there are two different problems mixed up:

1. Since about 2 weeks wrong "counters" are displayed. If a redirecting cat "Blah" contains 1 File (or 1 cat), one cat level up it is listed as "Blah (1 F)". Fine. If the file is removed from "Blah" the counter doesn't change, the cat page shows "Blah (1 F)" like before. Touching via pywikibot doesn't fix it, but if you open the cat page "Blah" simply using your browser and close it without any action the counter is displayed correctly as "Blah (empty)". The maintenance category mentioned above usually contains 20 or 30 files (maintained well by User:RussBot), because of that bug it increased to 800+ some days ago.
2. The 2nd problem exists for years: Cat pages that get assigned their subcats via templates are not updated, so https://commons.wikimedia.org/wiki/Category:Non-empty_disambiguation_categories sometimes contains hundreds of empty ones. If one touches the subcats the problem is solved. By this problem at least 50 categories are affected, primarily maintenance cats. For example some days ago https://commons.wikimedia.org/wiki/Category:Images_from_the_Geograph_British_Isles_project_needing_categories_by_grid_square did contain more than 3000 subcats that were tagged via template for speedy deletion, but none shew up there.