you probably hit on this taxonomy problem too

For free tagging this works assuming free tagging is enabled for the first vocabulary

$node_type = 'story';
$vocs = taxonomy_get_vocabularies( $node_type);
$voc = array_shift( $vocs);

$edit = node_factory_create_node( $node_type);

// assuming free tagging is enabled for first vocabulary
$edit['taxonomy']['tags'][$voc->vid]= 'a,b,c';

$nid = node_factory_save_node($edit);

See also the tests directory

This works too

$edit['taxonomy'][] = 9;

So the documentation must be updated accordingly.