Be default, the Home page will ALL categories. In order to show ONLY top level categories, you need to modify the theme-woocommerce.php (includes/theme-woocommerce.php) file.

To do this, search for the following code:

$params = apply_filters( 'mystile_homepage_product_categories_params', 'number=""' );

and replace it with this:

$params = apply_filters( 'mystile_homepage_product_categories_params', 'parent="0"', 'number=""' );

Note: This change may be overwritten by a Theme update.