Most states tax you according to where you live, not where you work. Several exceptions exist, though. One notable exception is New York State, which will tax you if your employer is based there, even if you don’t live there, unless it can be demonstrated that the employer needs you to live outside the state to do your job. (Google “NY convenience of the employer” for more info on that.)
I would talk with your HR department. It’s possible that they determined you are responsible for taxes in both states, and misfiled the paperwork.