This could happen when bundled products and simple products are mixed in the order.

To solve this, override the Invoiceservice.php from vendor/magento/module-sales/Model/Service/InvoiceService.php and change the below functions codes.

public function prepareInvoice(Order $order, array $qtys = [])
{
    $isQtysEmpty = empty($qtys);
    $invoice = $this->orderConverter->toInvoice($order);
    $totalQty = 0;
    $qtys = $this->prepareItemsQty($order, $qtys);
    foreach ($order->getAllItems() as $orderItem) {
        if (!$this->_canInvoiceItem($orderItem, $qtys)) {
            continue;
        }
        if (isset($qtys[$orderItem->getId()])) {
            $qty = (double) $qtys[$orderItem->getId()];
        } elseif ($orderItem->isDummy()) {
            $qty = $orderItem->getQtyOrdered() ? $orderItem->getQtyOrdered() : 1;
        } elseif ($isQtysEmpty) {
            $qty = $orderItem->getQtyToInvoice();
        } else {
            $qty = 0;
        }
        $item = $this->orderConverter->itemToInvoiceItem($orderItem);
        $this->setInvoiceItemQuantity($item, $qty);
        $invoice->addItem($item);
        $totalQty += $qty;
    }
    $invoice->setTotalQty($totalQty);
    $invoice->collectTotals();
    $order->getInvoiceCollection()->addItem($invoice);
    return $invoice;
}

private function prepareItemsQty(Order $order, array $qtys = [])
{
    foreach ($order->getAllItems() as $orderItem) {
        if (isset($qtys[$orderItem->getId()])) {
            if ($orderItem->isDummy() && $orderItem->getHasChildren()) {
                $qtys = $this->prepareItemQty($orderItem, $qtys);
            }
        } else {
            if (isset($qtys[$orderItem->getParentItemId()])) {
                $qtys[$orderItem->getId()] = $qtys[$orderItem->getParentItemId()];
            }
        }
    }
    return $qtys;
}

private function prepareItemQty(MagentoSalesApiDataOrderItemInterface $orderItem, &$qtys)
{
    /** @var OrderItemInterface $childOrderItem */
    foreach ($orderItem->getChildrenItems() as $childOrderItem) {
        if (!isset($qtys[$childOrderItem->getItemId()])) {
            $productOptions = $childOrderItem->getProductOptions();
            if (isset($productOptions['bundle_selection_attributes'])) {
                $bundleSelectionAttributes = $this->serializer
                    ->unserialize($productOptions['bundle_selection_attributes']);
                $qtys[$childOrderItem->getItemId()] =
                    $bundleSelectionAttributes['qty'] * $qtys[$orderItem->getItemId()];
            }
        }
    }
    return $qtys;
}

Once the changes will go live, the customer will have a complete invoice. None items will be missed.