Stating I owe $2,000 in NY State Tax

Hello,

 

I work for a non profit located in Vermont and as of August, used to be a NH resident. Due to owing the state of VT tax money last year, I allocated additional taxes to be taken from my paycheck. When I moved to New York at the end of August I did the same. According to TurboTax I owe the state of New York upward of $2000. How and why?? During my time with my company I worked remotely in NY and in person in Vermont