It sounds like the FTB got a copy of an income form for you (W-2, 1099, whatever) that had a different amount for withholding than what you reported on your tax return. Or possibly an employer or a pension plan sent them a different amount of money than what your W-2 or 1099 reported.
In looking at the letter, is there any hint as to which form (W-2,. 1099, etc) they are referring to? You can't start investigating until you know which form they are complaining about.
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