There is no software error. TurboTax does not indicate any penalties even if you actually make excess 401(k) contributions, so I suspect that you mistakenly entered the 401(k) contributions as IRA contributions under Deductions & Credits and you need to remove those incorrect entries . A 401(k) is not an IRA. Enter amounts shown in box 12 of the W-2s only in box 12 of TurboTax's W-2 form, nowhere else in TurboTax.
