yes, you need to amend 2016 return by not taking the deduction and including form 5329 to pay the 6% excise tax
you need to amend 2017 to pay the excise tax for that year because the excess remained.
you need to withdraw the money in the HSA before 12/31/18 to avoid the 6% tax for that year. even if you do. any income earned by the HSA must be included as other income on your 2018 return
Here's what IRS Publication 969 has to say about the excess contributions (contributions in excess of what is allowed):
Generally, you must pay a 6% excise tax on excess contributions. See Form 5329, Additional Taxes on Qualified Plans (including IRAs) and Other Tax-Favored Accounts, to figure the excise tax. The excise tax applies to each tax year the excess contribution remains in the account.
Any excess contribution remaining at the end of a tax year is subject to the excise tax. See Form 5329.
You also must withdraw any income earned on the withdrawn contributions and include the earnings in “Other income” on your tax return for the year you withdraw the contributions and earnings.
