Why should you expect to have it happen any differently than that? That's the normal way things are handled. If you submit a payment that is 1 cent or 20 bucks short of the amount, then the computer penalizes you the normal amount of a penalty for being late with your payment. If there is a snafu of any sort, whether it is your fault or theirs, you just have to call them up and explain the situation to a person. They will usually be accommodating to you even in situations where your fault was even greater than your situation was,(like they did for you) as long as you haven't called in with a similar situation over the last several months. This is normal everyday fair with credit card snafus that happen to anybody, in any given month. You are complaining about something that is normal to the board, and acting like you were wronged in some unforgivable way. You were not.
Let me guess, it was a Citibank card? They like to charge you interest and accrue it immediately, and put you through hoops to take care of the interest. The only thing you would have been wronged on, any more than any other card, would be if it was Citibank, and you had to jump through those hoops because it was Citibank.(I've had cards with Capital, Synchrony, Wells Fargo, and Chase. None of them did me like Citibank did.) No other credit card I have had, makes you jump through the hoops and argue, to get the interest alleviated if it is taken care of in a week or 10 days of when the payment was due. It just takes a little more arguing with Citibank. The rest of it, dealing with the computer, then calling them up and dealing with a person, if it is any amount short, for even 1 day, is normal.