It is not uncommon for box 5 amounts used on form 8959 to be higher than taxable wages (box 1). Living in one state and working in another will not affect the total W2, box 5 amounts. You would only enter one W2 for the employer which may have two state lines (box 15); one for NY and one for NJ, for example, with duplicated wages in box 16. However, that does not affect the box 5 amount or form 8959.
You would eliminate the duplicated wages (for used for income tax purposes only) when allocating in the state interviews.
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