Typically the NY taxable income for part year or nonresidents reflects the full year income based on state law. The NY tax is calculated based on your full year's income, and then prorated based on how much of your total income was earned in New York. So when you see the NY taxable income including the PA that's correct.
If you're using TurboTax desktop, you should be able to review your IT-203, page 3, lines 45 and 46 to make sure your tax is being prorated based on your income percentage.
