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As long as form 1040,  line 6a has your gross SS $ amount in it, then it would have to be something else.

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Like perhaps forgetting to enter some of your income in the main section, and the IRS caught the missing income.   

For instance, tax-exempt income (Form 1040, line 2a), isn't normally subject to taxation by the Feds, but does figure into how much SS ends up getting taxed and showing in line 6b 

____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*