Why was I not given credit for my rollover partial return (within 60 days) to my IRA when I even entered in the net amount for box 2a on the 1099-R?

I took a distribution of $10,000 and returned $7,000 within 60 days. The 1099-R shows the same gross amount in boxes 1 and 2a because we can still make contributions until April 15, 2018. I answered all the TurboTax questions regarding the rollover including box that asked for the amount of the rollover. When the income is shown, it is still on the gross amount.