The display of subcategories on category page (i.e. http://website/course/index.php?categoryid=49) doesn't have a distinguishing format to separate it from courses listed. In past versions, subcategories were separated in a box. Without the box, the subcategories sit right on top of the courses and make it navigationally confusing.
I've tested it in all default templates and it's universal.
- will be (partly) resolved by
MDL-31830 Replacement for the course and category management pages