Retirement tax questions

I filed the way TurboTax filled out NYC-208 for me (showing interest for the whole property) for 1996 and got a note from NY disallowing the deduction.  This year, TurboTax did the same thing so I got the instructions for the form and, the way I read it, I should only show 50% of the tax.  Wanted to check with others before sending in my tax return.  It would seem that TurboTax needs a correction (especially since it already knows this is a 2 family house and I live in one apartment).  How can we get TurboTax to chime in here?