If you received a 1099-SA in 2018, then when you enter it (well, you already entered it), when TurboTax asks if it was all for qualified medical expenses, answer "No" (even if it was).
Then when it asks how much was nonqualified, enter the amount of the 2016 excess.
You see, you withdrew the 2016 excess in error (according to the IRS) in 2018, so since this withdrawal is not considered a withdrawal for qualified medical expenses, you can tell TurboTax this.
This should add the 2016 excess to Other Income on whatever schedule that was on in 2018 (1?) and modify the 5329 to cut off the 6% penalty for that excess as well as add the 20% penalty in line 17b on the 8889.
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