If you have payroll contributions, they are automatically captured by Turbotax from your W-2. You do not enter them again later in the program. All contributions made by payroll deduction are considered "employee contributions" under the law and you should only separately enter contributions that you make directly to the HSA bank out of your own pocket.
Also, you must answer that you had a qualifying HDHP all year, or at least for the month of December, and no other medical coverage, including FSAs or spouse's insurance.
Your numbers don't quite add up either way, so you may have entered something else incorrectly. Check your W-2, what is entered in box 12 with a code W next to it?
If you already filed and paid the tax and penalty, you can file an amended return to correct your answers and get a refund.
