It's painful to be charged a one day rate for a 40 minute late drop. It used to be that agencies allowed a 59 minute grace. A couple years ago, most switched to a 29 minute grace. This is why if I think I'm going to have a 26 hour rental, I look at booking with my AMEX plat card. That allows a 4 hour grace.

OP, do you have a copy of your rental contract? Do you have a copy of your receipt? You should look and see what the terms were for the return. For example, was there a lower fee for the first hour than charging you an entire day's rental. You'll want to know those terms before you challenge the bill. Unfortunately, if the agency has been clear in the contract that you signed when accepting the car as to the late fees, you won't be able to challenge this no matter how unfair it feels.