Make sure you entered your employer contributions properly: Where do I enter my HSA contribution? On the Let's enter XXX HSA contributions screen, make sure Any contributions you personally made has a zero ($0). See the screenshot below.
Please click on Why is my HSA distribution taxable?
Also, click on Why am I showing an excess HSA contribution?
Other possible reasons why your refund amount may increase:
Another reason your refund may have gone up after you entered your Form 1099-SA is because a Health Savings Account (H.S.A.) can have up to three parts where you have to enter amounts and the way TurboTax does the calculations.
Part 1: When you enter your W-2, the amount in box 12, H.S.A. contributions, will be included as miscellaneous income (Form 1040 Line 21), be added into you taxable income plus a 6% excess contribution tax penalty will be added.
Part 2: When you enter your Form 1099-SA, your refund will decrease until you answer 'Yes, I spend the full amount on medical expenses'. The refund will go back to the amount before you entered your Form 1099-SA.
Part 3: TurboTax generates Form 8889 and you have to complete the questions so the the contributions on your W-2 are eligible and not taxable. When you answer that 'Yes, I was enrolled in a HDHP as of December 1, 2015' and 'Who was covered by this HDHP?' , your refund amount will increase or your amount due will decrease.
If the Part 3 questions are answered right after you enter your Form 1099-SA, it appears that that form caused your refund to increase.
Click on IRS Publication 969
Health Savings Accounts and Other Tax-Favored Health Plans .
[Answered edited 3-5-16 1:42 pm PST]
