I’m not sure that understand what are you trying to implement.
I don’t see any warning on the checkout page. So, explain in more details how can I reproduce this issue.
Besides, tell me if it works with default WP + WC + default theme? Or you have this problem only when our theme is activated. Because we are theme support and we can help you with issues related strictly to our theme. If some default WC functions do not work for you even with default theme you need to contact WC plugin support.