Where on the return are you concerned about seeing the city tax withholding? TurboTax will apply it to Form 1127 when you indicate that you are not a resident of the city. The treatment of it is "city tax" by the program is correct, as it is how the software knows where to put the form. The 1127 form is simply providing you with the technical definition of what you are paying.
Perhaps if we know more about where you are seeing the number that it appears incorrect we can provide additional reassurance? (It sounds like it may simply be on a summary screen, which is not part of any tax return.)
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