Hi,
If you have error messages with "alert-error", it indicates that you've activated the "use bootstrap design" setting of the HikaShop configuration so that HikaShop output HTML with bootstrap 2 classes, which are what the default Joomla template supports.
If you turn off that setting, HikaShop will use its own classes with its own CSS to display the messages and thus it will display correctly regardless of what your template is using.
If you want to keep the "use bootstrap design" setting activated but want to modify the class used, then you'll have to edit the function hikashop_display in the file administrator/components/com_hikashop/helpers/helper.php
However, I don't recommend that since you'll loose the change each time you update your HikaShop.