If you were covered by a workplace retirement plan and your modified AGI for the purpose of deducting a traditional IRA contribution exceeded the limit, the traditional IRA contribution was a permissible nondeductible contribution and your 2016 tax return should have included Form 8606 to report that. This became basis that carried over to 2017 and subsequently to 2018.
If your modified AGI for the purpose of making a Roth IRA contribution was above the limit, your Roth IRA contribution was an excess contribution subject to penalty. Your 2016 and, if the excess could not be applied as a 2017 Roth IRA contribution, your 2017 tax returns should have included Form 5329 calculating the 6% excess contribution penalty for each of these years. Assuming again that you cannot apply the excess as a 2018 Roth IRA contribution, you own another 6% penalty for 2018.
You are long past the October 15, 2017 deadline for recharacterizing the Roth IRA contribution made for 2016. If you are unable to apply the excess in the Roth IRA as a 2019 Roth IRA contribution, you must correct the excess by making a regular distribution of the excess from the Roth IRA with no adjustment for earnings. Because the excess is part of your Roth IRA contribution basis, the distribution will not be subject to tax or penalty on your 2019 tax return.
