Where did you fill out the payment arrangements for PA? Was it for PA or the IRS? Does it say you are getting a refund or paying in?
If you work in NY and live in PA it is very possible that you are getting a refund of your PA taxes withheld. Did you already file your NYS return? This should be done before your PA return. If you are getting a credit for taxes paid to NY on your PA return, then it would make sense that you are getting a refund as NY taxes are higher than PA taxes for the most part as PA has a 3.07% flat rate and NY has a graduated tax rate of 4% up to 10.9%.
When you file multiple states, you will fill out your nonresident states first, in your case NY. Then you will fill out your resident state, claiming a credit for taxes paid to NY on your PA return. Since NY tax rate is higher than PA's, you would not owe any taxes on the income you earned in NY to PA. You may still owe taxes on income you earned in PA though. You also would own NY if taxes were not withheld for NY.
If the non resident state had a higher tax rate than your resident state, your credit will be limited to the amount of tax you would have paid to your resident state. They will not give you a refund of the taxes you paid to the nonresident state.
Multiple States
File Non Resident State Return
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