You have a 6% excess contribution penalty on both your 2015 and 2016 tax returns. Since you did not already file a 2015 Form 5329, you must file it and pay the 6% penalty for 2015. Although the IRS will often accept Form 5329 without a Form 1040X, if you previously filed a 2015 tax return, it would probably be best to file it with Form 1040X since it affects the amount of your tax liability that should have originally been reported on your 2015 tax return.
If the excess was not withdrawn before the end of 2016, you also owe a 6% penalty on this excess for 2016. The penalty is due on the excess each year it remains in the account at year-end. In this case, after clicking the Continue button on the Your 1099-R Entries page you would indicate to 2016 TurboTax that you made excess contributions in a prior year that were carried into 2016. TurboTax will prepare 2016 Form 5329 to include with your 2016 tax return.
