State tax filing

Yes, I see that my NY State tax refund remains the same whether I enter the actual amount in line 16 or use the percentage option.  What I don't understand is what the impact is to me NJ State Tax return.  If I enter the actual amount on Line 16 in the NY State Tax return I receive a refund from NJ. But if I use the percentage I owe thousands of dollars to NJ.  My NJ W-2 shows that I have paid NJ State taxes for the portion of wages earned while I worked in NJ.  Using the percentage in the NY State Tax form aren't I being double taxed by NJ?