The reason that this happens is because the domain name on the security certificate will always be https://www.yourwebsitesdomain.com. If anything other than http://www.yourwebsitesdomain.com is in the URL when you go to checkout, then you will get this error. If your shopping cart software generated links are not going to www.yourwebsitesdomain.com, please contact technical support so that we can correct this error.
You can also go to Settings >> Site Security > Force site to use "www" prefix. If you set this to YES, then no matter what a visitor types in the for your URL (http://www.yourdomain.com OR http://yourdomain.com), they will automatically be directed to http://www.yourdomain.com. This will stop the issues with the security error.
Note: This ONLY effects stores that use their own SSL.
