Can a landlord charge a late fee after full payment has been received?

"The contract clearly states that tenants will be assessed a $50 late fee for failing to pay before the end of the 4th" Yes, you owe the $50. Just because the software did not automatically show the late fee does not mean you don't owe it. If you pay your taxes late, do you know how much you owe in Penalty and Interest? No, not even if it is paid online. You also were fully aware of the clause in the lease stating that payments made/received after the 4th are subject to a late fee. You were fully aware of the date when you paid it.

You should have handled any problem if you were withholding paying...earlier. If you pay late, you will owe a late fee. If they accepted your money after it was late, I always tell the renters that first the late fee comes out of what is paid no matter what is stated on the check and then the rest is applied to the rent. That could make rent even later...and my late fees continue and go up and one is charged daily until the rent is paid or according to local law...for fifteen days. All you can do is nicely plead your case to your landlord but don't be surprised if you are told you owe the late fee. When you don't pay on time...for any reason...you will get late fees.

Yes, legally you're SOL since you know the lease clearly states a late fee will apply to rent paid after the end of the 4th and you paid on the 5th. That said, if you didn't pay your full rent PLUS the extra $50 late fee from last month this month, you will get hit with another late fee tomorrow, since your rent payment would first be applied to the late fee and then the rest to rent, leaving your rent for May short $50. If you didn't pay the late fee with your rent, you probably want to go ahead and do that to avoid an additional fee this month.