先删除类别，然后插入

$options = array(
    'category_Id' => $_POST['product_category_id'][0],
    'product_id'  =>  'product id here'/* first category will be inserted only*/
);

$this->db->query("DELETE FROM product_categories WHERE product_id=". $options['product_id']); /* this will delete all categories assigned to $options['product_id']*/

$this->db->insert('product_categories', $options); /* will insert the first category from $_POST['product_category_id']*/

多更新，然后尝试此

$this->db->query("DELETE FROM product_categories WHERE product_id='product id here'";
foreach($_POST['product_category_id'] as $key => $product_category_id){


$options = array(
    'category_Id' => $product_category_id,
    'product_id'  =>  'product id here' /* first category will be inserted only*/
);    
    $this->db->insert('product_categories', $options);
}