I am also seeing the same issue as @ronniemarlofilms . My employer contributed $5000, below the threshold, and I was covered the entire year under a HDHP. TurboTax is indicating that the entirety is 'excess' exactly like OP's problem and saying I should withdraw it all to avoid 6% penalty.
Believe there is an issue with the software. Please address this when you can @BillM223
Edit: By continuing on, it appears that TurboTax is wrongly considering the amount entered in W-2 Box12 coded 'W' as taxable income. That should be tax-exempt.
