How To Remove Duplicate Menu Locations

You register an array of four menus.
If you reformat your code, you will see it.

[…]
array(
    'primary-nav', 
    __( 'Primary Menu'),
    'footer-nav', 
    __( 'Footer Menu')
); 
[…]

Adapt your code to an array with custom keys and you will be fine:

[…]
array(
    'primary-nav' => __( 'Primary Menu'),
    'footer-nav' => __( 'Footer Menu')
); 
[…]