@jtnguyen822 ,
Because the filing deadline for your 2019 tax return was extended to July 15, 2020, you could have received a distribution that was a return of contribution before the due date of your 2019 tax return, but that's not the distribution that you received. The simplest course of action is to treat the distribution that you received as a distribution of the excess after the due date of your 2019 tax return, making the excess subject to a 6% excess-contribution penalty on your 2019 tax return but allowing the gains to stay in the Roth IRA. This would have been the best course of action anyway if the gains at the time were more than something like 30%. Regarding the penalty, you could just file 2019 Form 5329 to report the excess and pay the penalty. Your 2020 Form 5329 would then show the excess carried in from 2019 and the code T distribution eliminating that excess for 2020. No further distributions are needed to correct the excess.
The only other potential alternative would be to treat the code T Form 1099-R as erroneous, calculate how much of that gross distribution would be considered an amount of earnings proportionate to the remainder of that distribution, treat that as a return of contribution before the due date of your 2019 tax return with the earnings being taxable on your 2019 tax return. For example, if the excess contribution was $5,000 and the gains were 25%, you could treat the $5,000 distribution as a return of $4,000 accompanied by $1,000 of gains. However, that would still leave a $1,000 excess contribution in the account subject to a 6% excess contribution penalty on both the 2019 and 2020 tax returns, so I doubt that this approach would be all that beneficial compared to the first approach. The viability of the second approach is also dependent on the examiner's willingness to accept it, with the fallback being the first approach if they don't.
