based on what you provided this shouldn't happen. assuming you filed timely and jointly for 2017, then entering the same agi for both of you is correct. you say entering $0 for both of you doesn't work. schedule C has nothing to do with the agi question (it's part of it). did you amend 2017 because you are supposed to use AGI as originally filed.
you can try contacting the IRS to see if they can( will) help. if that doesn't work out then your only choice is to paper file.
