"Can" they charge you these fees?? Of course, they did charge you.
Are you required to pay these fees?? Based solely on your post, probably not.
What should you do?? I would certainly try to discuss these fees with 'them'.
However, lets look at the 'real' situation:
I assume that they didn't accept your check due to previous problems with your checks. If correct, then they certainly have every right to demand payment by money order or cashiers checks. If you knew about this requirement beforehand, and decided to 'test' them by offering a check at the last minute, then they are probably correct in charging you a late fee, since valid payment was NOT made on time. Now, as a result of the delay in payment (and possibly due to previous problems) they sent you a "3 day notice". If it is their standard policy to charge you a fee due to the notice, then you will also be stuck with that.
So, now the ball is in your court so to speak. If you were absolutely 'fault-free' talk with the landlord or manager to try to resolve this problem. However, if any of my above assumptions are valid, then you need to decide to pay the fees or face another probable vacate notice.