Wrong drupal hook usage that leads to bad errors

You do this:

$item = module_invoke_all('taxonomy_menu_'. $op, $item);

which leads those errors:

# warning: Illegal offset type in isset or empty in /var/www/ademe-usine/drupal-dr/www/modules/taxonomy/taxonomy.module on line 1011.
# warning: Illegal offset type in /var/www/ademe-usine/drupal-dr/www/modules/taxonomy/taxonomy.module on line 1012.
# warning: Illegal offset type in /var/www/ademe-usine/drupal-dr/www/modules/taxonomy/taxonomy.module on line 1015.
# warning: Illegal offset type in isset or empty in /var/www/ademe-usine/drupal-dr/www/includes/common.inc on line 902.
# warning: Illegal offset type in isset or empty in /var/www/ademe-usine/drupal-dr/www/modules/locale/locale.module on line 362.
# warning: mysql_real_escape_string() expects parameter 1 to be string, array given in /var/www/ademe-usine/drupal-dr/www/includes/database.mysql.inc on line 321.

and this is because of the array_merge behavior in:

function module_invoke_all() {
  $args = func_get_args();
  $hook = $args[0];
  unset($args[0]);
  $return = array();
  foreach (module_implements($hook) as $module) {
    $function = $module .'_'. $hook;
    $result = call_user_func_array($function, $args);
    if (isset($result) && is_array($result)) {
      $return = array_merge_recursive($return, $result);
    }
    else if (isset($result)) {
      $return[] = $result;
    }
  }

  return $return;
}

which, technically, gives us as return when two modules implement the hook:

Array
(
    [tid] => Array
        (
            [0] => 20
            [1] => 20
        )

    [name] => Array
        (
            [0] => Actualité
            [1] => Actualité
        )

    [description] => Array
        (
            [0] => 
            [1] => 
        )

    [weight] => Array
        (
            [0] => 0
            [1] => 0
        )

    [vid] => Array
        (
            [0] => 6
            [1] => 6
        )

    [ptid] => Array
        (
            [0] => 0
            [1] => 0
        )

    [menu_name] => Array
        (
            [0] => menu-main-menu
            [1] => menu-main-menu
        )

)

So, there is two choices, either change the hook signature with a & to force ref, but no return (first patch attached) or use drupal_alter() (second patch attach), choose your weapon, but fix this.
PS: the first one is better is does not changes the functions names.