Which version? Should have been fixed since the 1.4.0I run into this error when trying to add a new prefix to an empty prefix group. I'm am running SEO2 1.5.0, I'll update it and keep you updated.
Look here to fix the error manually -> https://xenmade.com/threads/add-prefix-error-with-seo2-unknown-column-seo-in-field-list.38/