Apartment office loses my check then fines me for past due rent, what to do?

I have lived her for 5 months now and I have always paid the rent on time. The month before last I noticed it was taking unusually long for the money to be drawn from my account like it usually is after I drop off the check. Next thing I know I have an eviction notice plastered on my door for not paying. I take it to the office immediately and tell them I don’t understand bc I specifically remember dropping this check off. I had been paid early in the month and remember thinking how great it was to pay the bill off early! So I show the manager I have a check missing from my book and that I have the money in my bank account. She has me rewrite a check and says she will “do her best to get the fine waved” um ok thanks.. Two months later I get another notice on my door saying I owe $60 for the late fee. I am not sure what to do about this now. I know I should not have to pay a fine bc the office lost my check but I cannot afford to lose my place over such a petty argument. The only form of proof I think I would have is my bank statement showing I did have the money in my account at the time. What is there that I can do to get this cleared up?