We cannot see your returns in this forum but you will owe taxes when the deductions and credits (including taxes withheld) on your tax return do not reduce your tax liability to zero.
Generally, for NJ, from your NJ wages (W2, box 16) you will subtract a personal exemption (likely $1000), a $2500 deduction for NJ student loan payments, $10,000 for NJ tuition deduction and a property tax deduction based on your rent paid.
From your post with $46K of NJ income there will be some remaining NJ taxable income which is taxed by NJ and from that tax liability, the NJ taxes withheld (W2 box 17) are subtracted and the remainder is the tax owed.
Since, as you mention, NJ and PA have a reciprocity agreement taxes should only be withheld for your resident state (NJ) and you don't need to file in PA; there will be no credit for taxes paid to another state.
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