None of us here can see your tax return, so it's hard to know exactly what's going on. But for starters, if your main home is in Colorado, and your 3-month stay in New York was strictly temporary, then for tax purposes you are a non-resident of New York and a resident of Colorado. You are not a part-year resident of either state. Be sure that you don't indicate on the IT-203 that you were a part-year resident of New York. A part-year resident is a person who makes a permanent move from one state to another during the tax year.
New York taxes non-residents only on NY-source income. Income earned from work physically performed in NY is NY-source income. Did you work in NY during your 3 months there?
Also, in TurboTax, you must complete your non-resident state tax return before your home state tax return. If you don't do your state returns in the correct order, errors may occur.
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
