There is an option on categories to allow "Aggregate including subcategories". This can have the effect of double-counting grade items within sub-categories. It makes calculations very problematic.
No one can think of a valid use-case for this functionality.
A decision was made at the Gradebook workshop to remove this option and its functionality. Removing the option may affect sites potentially using this option. On upgrade, the use of this option needs to be detected and affected users (teachers in courses) need to be messaged with information about the change.