I would say you need to add the following rewrite rule in your foreach loop:
add_rewrite_rule('^'.$pt_slug.'/category/(.+?)/page/?([0-9]{1,})/?','index.php?post_type=".$post_type."&category_name=$matches[1]&paged=$matches[2]','top');
I would say you need to add the following rewrite rule in your foreach loop:
add_rewrite_rule('^'.$pt_slug.'/category/(.+?)/page/?([0-9]{1,})/?','index.php?post_type=".$post_type."&category_name=$matches[1]&paged=$matches[2]','top');