It should be OK if you indicated your proper residency situation in the MyInfo section (before he Federal tax section). NC allows you to file MFJ-Federal, and MFJ-NC for your situation, and only assign a sub-portion of your total $$ to NC based on what your wife earned in NC (I don't know what PA allows). When you start the NC section, from the very beginning, you will indicate you were a nonresident on NC who earned income in NC as a nonresident (even if you didn't, but some of it actually was your wife's) confusing eh?
((((I really don't like how the NC mixed spouse residency interview proceeds here...it has changed from prior years and tends to be a bit (or a lot) non-sensical in spots)))))
The big BUT....is that how you do assignment of the proper sub-$$ amount to NC is really confusing in the TTX interview....and also depends on whether your wife/spouse was a part-year resident of NC, or a full-yr resident of NC.
In either case, I recommend you switch to the Desktop/download Deluxe or Premier version of TTX, where you can go back and forth and look at the actual NC forms interactively with the NC interview. Plan to spend several weeks at it to get it right because the NC $$ allocations can be confusing, and you may have to mess with it some so that the $$ in the NC column (the "B" Column) of the NC D400 Sch PN are assigned properly. TTX uses a worksheet to feed into this schedule and whether only one column, or both columns of the worksheet are used will depend on whether your wife was a full-yr or part-yr resident of NC (and whether she worked or not).
When done, your NC D-400 should show your Federal AGI in line 6, and the total NC yearly income down to line 12b ....and line 13 should be a decimal multiplier that reduces 12b to line 14 which is the final actual taxable NC income based on what fraction (line 13) was earned/ or allocated to NC as NC income.
BUT..but..getting that right, really needs to be done using the desktop/download software on a full MAC (High Sierra 10.13 or higher) or Windows (rev 8 or higher) computer: