Use the on() function to bind to elements even new ones, otherwsie you have to continuously rebind the element.
jQuery(document).on("change",'select[id="warehouse-' + count + '"]',function() {
alert('hello');
var urlWareHouse = "<?php echo $this->url('stock', array('action' => 'populateLocationInWarehouse', 'controller' => 'Stock')) ?>";
url = urlWareHouse + '/' + jQuery('id="warehouse-' + count + '"]').val();
SelectBoxNullValue = "Select Location";
populateSelectBox(url, 'warehouse-'+count, 'location');
count++;
});