I ran into this in doing my part year return for NC. All of my federal tax exempt income was paid while a NC resident but only about 1% was NC tax exempt. I entered the split in the TT step by step, with the other 99% shown as "all other states" tax exempt. TT program did not transfer the non NC tax exempt income to all the places it was needed. I think it made it to D-400 schedule S but not to schedule PN (or possibly vice versa). I ended up going to the form and overriding the code to enter the amount where needed.
