It's not possible to have one instance of custom fields per quantity of the product selected. (not unless you recode the whole custom fields and add to cart handling as well as a big part of the product page display...)
It's far easier simply not allow the user to add products to the cart more than one at a time when needed.
To do that, you can add the code:
<?php
if(!empty($this->itemFields)){
$this->params->set('show_quantity_field',0);
}
?>
at the beginning of the file "quantity" of the view "product" via the menu Display->Views.