When you enter HSA contributions (for example, with a code W in box 12 on your W-2), by default, the IRS considers them to be taxable. They are not rendered tax-free until you complete the HSA interview later in the return. Only then will the contributions reduce your taxable income.
IRAs may function the same way (I haven't looked closely), in that contributions to an IRA may be considered taxable until TurboTax has had a chance to determine that the contribution was under the annual IRA contribution limit and allowable.
In any case, it is not a good idea to watch things like the Refund Meter too closely as you go through the data entry process because some things may not be calculated until much later in the return.