function my_posts_where( $where ) {

	$where = str_replace("meta_key = 'document_%", "meta_key LIKE 'document_%", $where);

	return $where;
}

add_filter('posts_where', 'my_posts_where');



$args = array(
'numberposts' => -1,
'post_type' => 'course',
'meta_query' => array(
    'relation' => 'AND',
    array(
        'key' => 'document_%_type',
        'value' => $document,
        'compare' => 'IN'
    ),
	array(
        'key' => 'form_of_edu',
        'value' => $form_of_edu,
        'compare' => 'IN'
    ),
	array(
        'key' => 'type',
        'value' => $type,
        'compare' => 'IN'
    )
)
);

$query = new WP_Query( $args );
$arr = $query->posts;

print_r($arr);