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If you were over-charged account maintenance fees and commissions by a brokerage and you took the fees as a tax deduction in previous years, you would need to include the amount in miscellaneous income.  In the past, those fees would have been a miscellaneous itemized deduction subject to 2% of your adjusted gross income.  That being said, there is a good chance you did not deduct those expense in the past but you would need to look at your old tax return.  

If they are related to stock transactions and you still own the stocks, you would need to decrease your basis for gain pro-rata on the stocks that were affected by the overcharged commissions and fees.   If you sold all the stocks involved, you would have realized capital gain for the amount of settlement and and would be reported on Sch D, depending on if it is long term or short term based on the holding period of the stocks sold.