You probably either:
1) Failed to enter the non-deductible contributions in the IRA contribution interview to produce a 8606 form reporting the non-deducitble contribution for the tax year that it was for.
2) Failed to enter the non-deductible "basis" in the 1099-R interview when entering the 1099-R.
3) The year end value of all Traditional IRA accounts was not zero so some or all of the distribution was taxable.
Method of entering a "Backdoor" Roth (years assume 2018 tax year):
This so-called “back-door Roth” method ONLY works if you have NO OTHER Traditional IRA accounts. If you do, then the non-deductible part must be spread over ALL accounts and cannot be withdrawn by itself. Only if you started with NO Traditional, SEP & SIMPLE IRA and ended up with a zero amount in ALL Traditional, SEP & SIMPLE IRA accounts will this Roth conversion not be taxable.