Did you possibly complete the state interview and then go back to the federal section to add another W2 ? If you did then you had to complete the state interview again for the new info to transfer correctly.
If you believe you used the program correctly then put in an accuracy claim :
Any calculation errors on the part of TurboTax are covered under the Accurate Calculation Guarantee. TurboTax will pay any penalties and/or interest due to a calculation error but not any taxes owed. The Guarantee does not cover any user entry errors or omissions.
See this TurboTax support FAQ for the 100% Accurate Calculation Guarantee - https://ttlc.intuit.com/questions/2566201-what-is-the-turbotax-100-accurate-calculation-guarantee
See this TurboTax support FAQ for submitting a claim - https://ttlc.intuit.com/questions/1901269-how-do-i-submit-a-claim-under-the-turbotax-100-accurate-ca...
See this TurboTax support FAQ for documents needed to submit a claim - https://ttlc.intuit.com/questions/1901060-what-documents-do-i-need-to-submit-a-claim-under-the-turbo...