Hi,
I've never seen such problem with HikaShop.
And until the end of the checkout the products are correct in the cart.
So this looks like a problem with a plugin implementing the onBeforeOrderCreate or onAfterOrderCreate triggers on your website.
As the payment plugin you're using is not a plugin we developed ourselves, I would recommend to first try with a standard payment plugin like PayPal or check or bank transfer and see if you also have the issue.
If you do, then it must come from a plugin of the group "hikashop" or "system" and I would recommend to do some tests by disabling the plugins one by one and testing each time.
If you don't, then it must comes from the payment plugin and you should check with the payment plugin developer for help as there is probably something to fix in the plugin.