there is a problem, when mixing CPT and taxonomies (like e.g. http://money.mediacentrum.cz/reference/?kraj=ustecky-kraj&produkt=&branze=chemicka-vyroba), it than throws
Notice: Trying to get property of non-object in /var/www/vhosts/money.cz/httpdocs/wp-content/plugins/wordpress-seo/frontend/class-breadcrumbs.php on line 226
Actually it is a wordpress bug (#20994, #18614, #19035), so it is up to you if you will make some workaround just for your breadcrumb plugin.
I'm solving it on my site by filling $post_type_obj->labels->name on such pages. And i have noticed one other bug - you are using on that line 226
$archive_title = $post_type_obj->labels->menu_name;
IMO it would be much better to use "name" instead of "menu_name" label, as it is standard in whole WP installation, where the name of post_type is needed. And btw menu_name is optional (but it may be automaticaly filled by "name", i am not sure)