If you live in NJ and work remotely for a company in NY, but do not go into the office, then your employer would only need to withhold taxes for your home state of NJ. You do not need to file a NY non-resident return if you never step foot in NY.
As long as you meet the Convenience of the Employer test, which most people do, you would not be subject to NY taxes, only NJ taxes. So your employer is doing this correctly.
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