Hi, @Justhero , thanks for the question!
So first, I want to be clear on our terms, to avoid confusion. If your income is reported on a 1099, then you are not an employee. You are a self-employed individual. Therefore, the company is not your employer, but rather your customer, if you will.
Based on that fact, you should only be taxed in states where you actually performed work. This work you did for the company, did you perform that in their state, or yours?
As to the Credit for Taxes Paid to Other States, you have to claim that on your resident state return in order to receive it. TurboTax has a section for that. If you did not file that way, then you should amend your return. This article shows how. In your case, you would only have to amend the state return.
Hope this helps, please let me know if not!
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