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What state are you in? How much have the deducted from your security deposit? When you say you paid first month, last month and one month's security deposit does that mean you were late paying the next to last month of the lease late or were you paying the last month's rent late even though you had prepaid it?
Two points. First, if you pay first and last month plus the security deposit then you did not have to pay the last month. Review your lease to see whether it says two months security or first and last month. The second point is that just because the landlord charges you for something does not mean you have accept it. You have the right to go to small claims court to challenge the deduction. You are entitled to recover double the amount of your security deposit that was wrongfully withheld. The items you should seek are the amounts you dispute about cleaning as well as the $100 late charge because there was no late payment. The amount you calculate as due you should be doubled because of youor right to recover twice the amount wrongfully withheld.
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