What do you mean "doubling W-2 amounts"?
Are you saying that the taxable income in each state is twice what it should be, or are you just saying that the your full income is appearing as state income on your W-2, making you think that you are being fully taxed in both states?
Generally, in the case of New York and New Jersey, you report to full amount of income in the non-resident state, then the tax from the non-resident is used as a credit to the resident state. So, yes, the income appears in both states, but because the the credit, you are not double-taxed.