Order total incorrect

On a kickstart site I have an order with a mismatch between the number of items in the order and the number of elements in the order total array (relevant section of the array from the order is at the bottom of this post ).

I haven't been able to recreate the problem with backups from the just before the order was created & completed but the customer ended up with an item in their completed order without any related charge.
Any idea what would cause this?
I guess there should be a check at some point in the order process to make sure that every item has an entry in the commerce_order_total array?

[commerce_line_items] => Array
        (
            [und] => Array
                (
                    [0] => Array
                        (
                            [line_item_id] => 3352
                        )

                    [1] => Array
                        (
                            [line_item_id] => 3353
                        )

                    [2] => Array
                        (
                            [line_item_id] => 3354
                        )

                )

        )

    [commerce_order_total] => Array
        (
            [und] => Array
                (
                    [0] => Array
                        (
                            [amount] => 2995
                            [currency_code] => NZD
                            [data] => Array
                                (
                                    [components] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [name] => base_price
                                                    [price] => Array
                                                        (
                                                            [amount] => 2604
                                                            [currency_code] => NZD
                                                            [data] => Array
                                                                (
                                                                )

                                                        )

                                                    [included] => 1
                                                )

                                            [1] => Array
                                                (
                                                    [name] => tax|gst
                                                    [price] => Array
                                                        (
                                                            [amount] => 391
                                                            [currency_code] => NZD
                                                            [data] => Array
                                                                (
                                                                    [tax_rate] => Array
                                                                        (
                                                                            [name] => gst
                                                                            [display_title] => GST
                                                                            [description] => Standard NZ GST for retail customers
                                                                            [rate] => .15
                                                                            [type] => vat
                                                                            [rules_component] => commerce_tax_rate_gst
                                                                            [default_rules_component] => 1
                                                                            [price_component] => tax|gst
                                                                            [calculation_callback] => commerce_tax_rate_calculate
                                                                            [module] => commerce_tax_ui
                                                                            [title] => GST - Retail
                                                                            [admin_list] => 1
                                                                        )

                                                                )

                                                        )

                                                    [included] => 1
                                                )

                                            [2] => Array
                                                (
                                                    [name] => flat_rate_free_shipping
                                                    [price] => Array
                                                        (
                                                            [amount] => 0
                                                            [currency_code] => NZD
                                                            [data] => Array
                                                                (
                                                                )

                                                        )

                                                    [included] => 1
                                                )

                                        )

                                )

                        )

                )

        )