I had same problem few months ago. As far as I remember problem is that Categories few displays links to subcategories pointing to category articles list when your subcategory menu item points to category articles blog. For Joomla those are 2 different pages thats why they have 2 different urls. Solution for this are two:
Easy
Make every subcategory menu item pointing to category articles list
Better
Edit categories list view so every subcategory url will point to category blog view not category articles list