If you shorted the minimum payment due, I believe the new CC laws state that they can charge you a late fee but can't jack your rates if it's the first time you've been late. Universal default (other CC's raising your rates because you were late on a seperate CC or loan at a different CC company or bank) is also banned, so your other cards won't be affected either. So all you need to do is call the CC and explain, odds are they'll reverse the late fee and then you can just send in the $9.
If you pay off your CC's in full and your payment was short $9, it get's trickier. There is no late fee of course, as you paid well over your minimum, but then the interest starts tolling because you didn't make full payment. To calculate interest they use your average daily balance, so you'd pay interest not on the missing $9, but your total balance divided by days in the billing cycle. Depending on your balance and interest rate, this could cost you a fair amount of money. They don't have to waive that, but of course it never hurts to ask.