Register and enqueue Magnific Popup (http://dimsemenov.com/plugins/magnific-popup/) scripts and styles, rather than calling them explicitly in the HEAD or footer. See http://ajtroxell.com/use-magnific-popup-with-wordpress-now/ for instructions on adding Magnific Popup to your WordPress theme or child theme.

enqueue-magnific-popup.php

<?php
//Add this to your functions.php file in your theme or child theme
add_action('wp_enqueue_scripts', 'enqueue_magnific_popup_styles');
function enqueue_magnific_popup_styles() {
	wp_register_style( 'magnific_popup_style', get_stylesheet_directory_uri() . '/magnific-popup/magnific-popup.css' );
	wp_enqueue_style( 'magnific_popup_style' );
}

add_action('wp_enqueue_scripts', 'enqueue_magnific_popup_scripts');
function enqueue_magnific_popup_scripts() {
	wp_register_script( 'magnific_popup_script', get_stylesheet_directory_uri() . '/magnific-popup/jquery.magnific-popup.js', array( 'jquery' ) );
	wp_enqueue_script( 'magnific_popup_script' );
	wp_register_script( 'magnific_init_script', get_stylesheet_directory_uri() . '/magnific-popup/jquery.magnific-init.js', array( 'jquery' ) );
	wp_enqueue_script( 'magnific_init_script' );
}
?>