If you are using subcategories, by default a main category will display both the subcategory links and a selection of products from all the subcategories.  If you'd like to change this to display only the subcategories, here's how:

• Login to your store admin

• Click "Catalog Setup" from the links on the right side

• Scroll down to where you see "Main Categories" on the left

• In that drop down choose "Categories"

• Scroll down more and click "Update Variables"