When you enter your Form W2 information in the "Job/W2" topic the income in box 1 has already by reduced by the amount in box 12 for your HSA contribution code W. So you should not enter any other HSA contributions in the HSA interview unless outside of that employment contribution you then contributed "more".
If after entering your W2 which has 7200 (the maximum allowed) deducted already, you then, in the HSA interview, enter another amount as a contribution you made, then you have exceeded the maximum and are penalized which is why your refund goes down.
Any amount entered via your W2 box 12 is treated as employer contributions even if it is withheld from your pay. The bottom line is it is not taxable income and is subtracted from your box 1 amount already.
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