As you realize, the additional HSA contribution should not increase your taxes due.
Note, however, that when you initially enter contributions such as on the W-2, that the IRS considers these contributions to be taxable, until there is a completed 8889.
The 8889 is the report that determines the annual contribution limit, and whether the contributions and distributions are tax-free or not.
But until you complete the HSA interview (that is, go all the way until you are returned to Your Tax Breaks), the 8889 is not complete.
This is why it's not a good idea to pay too close attention to the tax due, because sometimes TurboTax has to delay making a calculation until several screens have passed.
Complete the HSA interview and see if the extra contribution is rendered tax-free.
