Letter from IRS " Your Tax return doesn't match the information on file" on 2016 Form 1040. Missing State Income Tax Refund, Social Security. Both were reported.

[Critter]

If you disagree with the IRS then respond and show them proof that they are wrong ... send them a copy of the return you filed with those items highlighted.  But ... if you added these things after you had filed the original return then they may not have gotten the changes if you didn't mail them a copy of the amended return.