I suspect that you have received single sheet containing two separate 2019 Forms 1099-R (each line being a separate Form 1099-R), one for the return of the excess Roth IRA contribution made for 2018 (code JP in box 7) and another for the distribution of the excess contributions made for 2016 and 2017 (code J).
The excess contributions for 2016 and 2017 must be reported and the penalties paid by filing 2016 and 2017 Forms 5329. The 2016 Form 5329 would show the 6% penalty on just the excess contribution made for 2016 and the 2017 Form 5329 would show the 6% penalty on the sum of the 2016 and 2017 excess contributions.
The distribution before the due date of your 2018 tax return of the excess contribution made for 2018 was reportable on your 2018 tax return if there is any amount shown in box 2a of the code JP Form 1099-R. If the box 2a amount was not previously included on line 4b or your 2018 Form 1099-R you add this by amending your 2018 tax return to add this code JP Form 1099-R. You would also need to make sure that your 2018 Form 5329 show only a 6% penalty on the sum of the excess contributions made for 2016 and 2017, not the excess contribution made for 2018 that was returned before the due date of your 2018 tax return.
