My crystal ball is out for a tune up so I can't see your rental agreement, but I am going to guess it says there will be a $50 fee if your rent is late and that the $50 in question shall be considered additional rent. In this case, you are not being charged for the 3 day notice, instead, the $50 is a late rent charge.

Let's assume your rent is $500 per month, but you only make a $300 partial payment. You are now late, incurring the $50 fee on top of the $200 outstanding balance. You now owe $250. If you fail to pay the extra $50 when you pay the remaining $200, you are still $50 behind in your rent.

Let's say you pay the full $500 the following month. $50 is applied to what you owe from the past month. This means you have only paid $450 towards the current month, incurring another $50 late charge.

This will continue each month until you catch up on all your late fees.