The most common reason people see small discrepancies in the tax calculation is because they have some qualified dividends, capital gains distributions and/ or long term capital gains.
If you have qualified dividends, there will be a number on line 3a on your 1040. If you have capital gains, the number will be on line 6. If you have numbers in either of those places, your taxes are being calculated using the Schedule D worksheet.
If you look at line 12 of your Form 1040, you may see other reasons why your tax rate may be slightly different. If one of the boxes is checked, your tax was calculated on the form indicated.
If you have a Schedule 2 in your return, that may show additional taxes that you have to pay.
As far as the Massachusetts Schedule B, line 1 asks for both the amount from 2a and 2b of Form 1040.
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