You can change the box 16 amount for New York (NY) wages so that only the amount taxable from NY sources is included in the NY nonresident return. You have pay stubs to back up your entry. Try this, then go through the NY and the Pennsylvania (PA) return to complete the returns.
The state interview should allow an adjustment but this may make it easier to finish your return. The only criteria is to pay tax on the correct amount so correcting the W-2 should produce the results.
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