Go to Sch D, at the top click 1099B worksheet, scroll down to the Entry lines and double click on one of them, this worksheet opens

I filled in the employee stock  worksheet but the program is still now double counting the income as it is already in the W-2 and should not be reported as a capital gain

If they sold all of the stock whose value was in their W-2, the W-2 inclusion is the basis for the 1099-B transaction.

It's your data entry that is causing doubling; not the program.

sometimes there is a supplement schedule to the 1099-b with the cost basis adjustments on it.