Carrying over Late Fees..

Ihave not had a lease since 2003 and i am a mnth to mnth tenant on the property in question.
I was out of town on a family emergency and dropped off my rent check 1st thing on the morning of 6/9. 2 days later, get a call the property mananger that tthey had already filed a suit against me on the 5th and i owed late fees as well as filing fees that i needed to pay. a week later, in court, i was told by the property attorney that the case was withdrawn since i had paid my rent. I thought that was the end of it. In october, i paid my rent on time. i received a letter a week ago from the property manager last week that my rent for october had been applied to the late fees for september and that i now owed late fees for october because my rent was short the amount that was deducted for the sept. late fees and ontop of that, I was also charged late fees for october because the rent was short. So at the end of the day, I owe the amount of rent that was deducted for sept. late fees, and i owe late fees because the rent was incomplete as a result of their taking part of the rent payment.
My question is this: is this legal? can a landlord do this? and does it make a difference that there is no current lease since the lease expired in 03' and it has become a month to month tenancy?
Any help on the issue will be greatly appreciated. Thank you.

You can argue that that was not what you agreed. And sue them for the fees in small claims court if you have to.