Hi,
When you're on the checkout and you get an error, as everything happens in AJAX (dynamically, without the whole page changing), the Joomla messaging system cannot display the messages. In that case, it's HikaShop which displays the messages itself.
However, we normally want to let the template display the messages so that they can be styled by the template.
Since you don't have the problem with another template, it's probably an issue in your template.
I would recommend to contact your template provider and give them precise instructions to reproduce the issue so that they can have a look at it.
We can have a look at it too. If you need to provide private information, please use our contact form and include a link to this thread along with the instructions to reproduce the issue:
www.hikashop.com/support/contact-us.html