HSA: Refund up after 1099-SA?

My refund went up after I entered in my HSA distribution details.  They were all for qualified medical expenses but I don't understand what would cause my refund to increase.  This money was already contributed to the HSA account pretax which is where I thought the tax advantage occurred.  How then does my refund go up after entering in my 1099-SA info?  I could see it going down if I took some non-qualified distributions but not up.