In _simplenews_scheduler_new_edition() there's this:

  // Store taxonomy terms to save later to the node.
  $terms = $node->taxonomy;

  // ... later
    // Now save it as a new node.
    node_save($node);
    // Save taxonomy terms.
    taxonomy_node_save($node, $terms);

node_save() will save the taxonomy terms anyway. There's no need for taxonomy_node_save() -- that's called by node_save() via the node api anyway.