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"
And that will change your display.