Probably. If you live and work in the same state, that is where you are taxed. You are not taxed, in general, in the state where your company is located (with one caveat that I'll describe later). So if your state's tax return is currently saying that you owe, that is likely the correct result. However, in most cases, if you did have taxes taken out to another state, you can get these back by filing a tax return with zero income for mistaken withholdings.
There is one exception to this general rule. If you are working from home as a telecommuter, and the company you work for is in NY, NJ, PA, DE or NE, you are taxed where your company is located, in addition to your home state. In this situation, you would file a nonresident return for the other state where your company is located, and then file the resident return for your state. In this case, your home state will give you a credit for the tax you paid to the other state for the income earned there, and you should have a lower tax liability (or maybe not owe at all) in your state.
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