Little hack, which solved the problem. Go to /wp-content/plugins/yith-woocommerce-ajax-navigation/includes/functions.yith-wcan.php and replace
Old code:
if ( defined( 'SHOP_IS_ON_FRONT' ) || ( is_shop() && ! is_product_category() ) || is_product_taxonomy() ) {
New code:
if ( is_shop() && ! is_product_category() ) {
