This is not only standard shopping cart functionality, it's how Kentico's shopping cart functions as well. When you go to pay for your items by clicking Checkout, it converts the shopping cart items into an order so the order can be processed by the payment provider.
Unfortunately, it seems the cart is taking the user to another page to do this so what you could do is move the actual payment provider to the same page and when the click the "pay now" button, it will create the order and process the payment then you won't have any issues.