The banks will look for any excuse to charge you a fee.
A few years ago, I wanted to close my old checking account (which had a minimum balance). At the bank, they told me, "Write yourself a check for the amount in your account, deposit it into your new account, and your old account will be automatically closed." So I did. A couple of weeks later, I got what I thought was my final statement from my old account. It read: "Account balance: $0.00. Penalty for being under minimum balance: $20. Overdraft fee: $5. New account balance: -$25.00. Please remit."

Took me a while to straighten that one out.
I agree, banks should make things clearer to their customers, but it's so commonplace that deposits made after a certain time are processed the next day, that they just assume you know.