Just a guess but was the cost of the equities included on the Form 1099-B that you downloaded? If not, then the program has to assume that the equity had 0 cost to purchase and the sale price constitutes a gain.
Yes, not only was the cost basis included but TurboTax shows the capital gains and losses correctly when I view the 1099-B section. The problem seems to be that it is including a phantom gain, and I have no way to see it.
The gain could be coming from capital gain distributions as reported in box 2a on a Form 1099-DIV you entered:
The problem is that any capital gains distributions were picked up correctly by TurboTax when it downloaded the documents. However, I have solved the problem: I bugged out of TurboTax Online, cleared the return (which I could only do from Safari and not from MS-Edge), and purchased TurboTax Desktop. It handled all capital gains correctly and saved me almost $6000 over TurboTax Online!