I contributed to a Roth IRA in 2016, then later in the year I needed to purchase my first home. My understanding was I could use that amount without penalty.

I do not see a way to enter contributions from the current year when going through the 1099r. I deposited $2,000 in March, then in September came around, I withdrew $1,500 for purchasing the home.  It seems to be penalizing me even though the amount withdrew is less than the contributions.