Actually, the Products catalogue listing one subcategory looks correct, since it is listing from the Catalogues page (index.php?page=catalogues) which includes the catalogue itself as the main category. The Links catalogue looks to be correct on this page as well. But the subcategory counts within the Links catalogue pages (index.php?page=catalogues&type=category&catalogue_name=links and index.php?page=catalogues&type=index&id=links) are not right after adding some subcategories.

I also noticed Content>Links>Links Home (index.php?page=catalogues&type=browse&id=2) doesn't link to the Links Home page and instead it displays a page listing all of the catalogues.

Both issues fixed.