fix_paged_homepage.php

<?php
//Fix homepage pagination
if ( get_query_var('paged') ) {
    $paged = get_query_var('paged');
} else if ( get_query_var('page') ) {
    $paged = get_query_var('page');
} else {
    $paged = 1;
}

$args = array('post_type' => 'custom_post_type', 'paged' => $paged ); // Args for loop

$temp = $wp_query; 
$wp_query = null; 
$wp_query = new WP_Query(); 
$wp_query->query( $args ); 

while( ...