Federal return: Under the summary “Deduction & Credits” section, what is shown in the software for federal and state income tax withholdings are different than what I entered from my W2. The local income tax is correct.

Is that one single W-2 the absolute only source of income you reported on  your tax return? (probably not) Keep in mind that what you're looking at is a "summary", not a "all the fine details" screen.  The summary will include any taxes paid to the IRS/state by any means. For example, if you paid estimated taxes to the IRS, that amount is included in the summary.

@Lizy  

IF..if you are using the Desktop software. 

...............(Can also get with the Online software, but a bit more involved)

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Anyhow...with the Desktop software :

Switch to "Forms Mode" and open the Federal Tax Payments Worksheet.

That worksheet breaks down all the withholding by form type...and you can see if it came from some form you didn't consider.    IF any line there is wrong, you would go back to those form-types and check each for entry errors.

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