Another customer found that the dollar figure (ending in 51 cents) was rounded up to the next whole dollar, triggering an error. By dropping the number in the program by 2 cents, the error went away.
Since the employer has to either round the SS tax up or down to the nearest penny on each paycheck, it's possible that the total amount of SS tax collected from 52 or 26 paychecks will be a few pennies more or less than exactly 6.2% of the year end gross taxable amount. This is not something the employer can or should correct. But apparently Turbotax is very sensitive. If the exact tax at the end of the year ends in (lets say 45 cents), but the employer collected 51 cents due to rounding issues, and turbotax then rounds it up to the next whole dollar, it suddenly becomes a red flag. Turbotax is wrong in that case (too sensitive), not the employer.