Because your wife is a resident alien, she should have received a 1099-INT not the 1042-S. You may want to contact the bank and see if they require a W-9; if they have not already filed the 1042-S with the IRS they may be able to make the correction and return the withholding. (They also can file a corrected form with the IRS that zeros out the 1042-S and then issue you a proper 1099-INT.)
If the bank is not able, you still can add the information if her tax identification number on the 1042-S is the same as on the tax return. Make the entry in TurboTax on the 1099-INT screen, and check the box that "My form has info in other boxes (this is uncommon). Enter the withholdings from the 1042-S in Box 4 for Federal income tax withheld. The 1099-INT entry is not sent to the IRS through TurboTax, it is just used to record the interest income in the correct place on the tax return.
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