This is what's happening in the app from what I can tell:
TurboTax has $6000 on line 1 of Form 8606. I think it's removing the $3000 over contribution from this line because I answered that the $3000 withdrawal from the Roth was to correct the over contribution in the traditional IRA?
So when TurboTax gets down to Part II in form 8606, it puts $9000 for the amount converted from Traditional to Roth on line 16, $6000 on line 17 (contributions to traditional IRAs), and $3000 on line 18 (taxable amount).
