The 5329 calculates for HSAs the penalty for excess contributions that are being carried over to next year (the form does a lot of other things, but this is what concerns you).

If you carry over an excess HSA contribution to next year, then the penalty is 6% of the smaller of your carryover or the value of your HSA at the end of the year - this is why TurboTax is asking this question.

Evidently, in the HSA interview, TurboTax told you that you had an excess HSA contribution and you said that you were not going to withdraw it by the due date of the return. On the next screen, TurboTax should have asked you several questions, one of which was the value of the HSA on December 31, 2017.

It seems that you skipped this screen or just left the HSA interview without finishing it.

Please go back to the HSA interview (Federal->Deductions & Credits->Medical->HSA MSA Contributions) and go all the way through the interview to the end.