Your situation requires you to file two returns: a Puerto Rico return and a US return. Although Puerto Rico is a US Commonwealth and runs on the dollar, income from Puerto Rico is considered to be foreign income for tax purposes. As such, you will pay tax in the United States on this income, although you may claim a credit for the tax you pay to Puerto Rico on the same income.
Since you are not considered a bona fide resident of Puerto Rico, you want to prepare the Puerto Rico return first if possible. This is to determine the US Credit. Your credit is not based on tax withheld, but rather your tax withheld minus refund or in addition to additional tax due. To prepare the return for Puerto Rico, you might want to visit this website as the Puerto Rico return is not supported in TurboTax: http://www.hacienda.gobierno.pr/individuos/contribucion-sobre-ingresos/informacion-para-radicar-la-p... (This website is in Spanish. There was no translated website, but that page has the e-filing providers for a PR return). You may also dial the phone number provided on that site for additional assistance.
Once complete, follow these instructions to enter the Puerto Rico income in TurboTax: https://ttlc.intuit.com/replies/3290703
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