Why do you think that the HSA contribution is double-counted?
The first thing that comes to mind is that you put your payroll deduction for your HSA as a "personal" contribution in the HSA interview even though the instructions asked you not to. This is a common source of confusion for taxpayers who don't realize that you should not enter any part of the Code W (in box 12 on your W-2) amount anywhere in your HSA interview, or else you will indeed doubling your HSA deduction.
Of course, you may have meant something else, so come back if necessary and tell us in more detail what is happening.
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