I am puzzled. It's a bit difficult to see what is happening on your return, because the sanitation process obscures quite a bit, but I see four 1099-Rs, every one of which is listed on the federal return as a pension, not an IRA.
From what I see, three of the four 1099-Rs show to be from tax-exempt sources (I assume that that is correct), however, in the Massachusetts interview, there is a series of screens dealing with pension income. There is one screen that says "Pension Adjustment - Federally Taxable" and the number in the box is primarily that of your largest 1099-R, not the sum of the three 1099-Rs that appear to be tax exempt. Did you put that number there? If TurboTax preloaded it, why did you not change it when you saw it?
Instead of being in the 1099-R interview (where this sort of problem usually is), I would look in the Massachusetts interview at the various screens dealing with your pensions.
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