When you made the contribution for your HSA in early 2017 (OK as long as it is before the due date of the return), did you specify to the HSA administrator that this $3,350 was for 2016 not 2017? If not, the default action by the HSA administrator would have been to apply it to 2017.
If they applied it to 2017, then you should not have taken the "deduction" on your 2016 return.
Since it has been a year since these events occurred, I think that it is too late to get the HSA administrator to change the 2017 contribution to 2016 as it should have been, so you will have to amend your 2016 return to remove that "deduction".
Don't change the entry for 2017, because that would be making two errors instead of one - although the net effect may be close to the same (it depends on your marginal tax rate among other things), if the IRS notices the discrepancies, they will make you amend both returns.
Just leave the contribution as is for 2017, and go back and amend your 2016 return. Note that interest is running on the amount that will be due on 2016, so don't put it off.
