The excess IRA investment was solely contained in a new 2018 traditional IRA. The end of year 2018 value of that IRA was less than the investment. The IRA was closed in February 2019 and the total value transferred to a brokerage account. However, the total amount in the IRA at that time was less than the initial amount invested (value of stock declined). TurboTax compares the two amounts and concludes there is still an excess invested in the IRA, which is actually the loss resulting from closure of the IRA.
In the IRA contribution section when it asks of the excess was removed, say yes and enter the amount of the excess removed (the contribution amount) not accounting for any gain or loss. The excess is what it was at the time of contribution so that is what must be removed to cancel the excess.