Your 2016 excess removed in 2018 was required to be done by a regular taxable HSA contribution, code 1 in box 3 of the Form 1099-SA and indicated as not used for medical expenses. Entering this Form 1099-SA into TurboTax will result in the amount appearing on Form 5329 line 44 to be subtracted from the amount on line 42. This should result in lines 46 and 48 having zeros.
This amount not used for medical expenses is taxable (Form 8889 line 16) and subject to early-distribution penalty (Form 8889 line 20) in under age 65.