In Part I of the New York State Wages/Self-Employment Income Allocation worksheet, the amount in the New York Wages column comes from box 16 of your W-2. It's not clear whether you looked at the box 16 amount in the W-2 as entered in TurboTax. If you looked at the actual W-2 that you got from your employer, it's possible that it was entered incorrectly in TurboTax. If you imported the W-2 it's possible that an error occurred in the importing.
Are you looking at the forms and worksheets in forms mode in the CD/Download TurboTax software? If so, what color is the incorrect number on the New York State Wages/Self-Employment Income Allocation worksheet, and also in Column D of the Part-Year Resident/Nonresident Allocation Worksheet? If the number is red, that means it's an override of the amount that TurboTax calculated.
