The verification question "Do you have any employees who are exempt from any part of Medicare or Social Security taxes?" impacts this warning. If you employ individuals who fall under this category, indicate "Yes" as the answer to this question.
Once in the W-2 grid, you may still receive the warning, "Box 3 (social security wages) + Box 7 (social security tips) cannot be zero", however, with that previously mentioned option selected, you will now have the option for "Continue without Correcting". You can then continue processing your W-2s.