Don't look at the New York tax as soon as you enter your spouse's income in the federal section. Wait until after you go through the New York interview and see if you still owe New York tax.
Double-check that you correctly entered the NY information in boxes 15, 16, and 17 of your own W-2. Also make sure that you did not accidentally select NY in box 15 of your spouse's W-2.
In the New York interview, make sure that you are filing as a nonresident.
When TurboTax asks "Who has New York Source Income?" make sure you select that you had the only New York income (if that's true).
After you go through the New York interview, look at page 2 of Form IT-203. There are two columns for income. The left column (Federal amount) should show you and your spouse's total income, from your federal tax return. The right column (New York State amount) should show only your New York wages. Are those two columns correct?
The tax calculation on the New York nonresident return does start off with your total combined income. It first calculates the tax on your total income. Then, on line 45 of Form IT-203, it calculates what percentage of your total income is from New York. Line 46 then applies that percentage to the total tax. That's how it apportions the tax to your New York income.
