Never seen this before - call and ask. See what the CSR says.
Most creditors do this if your balance is under a certain amount, say $1.00. It's to save them from the expense of processing a payment exceeding the payment.
What you are seeing is the other side -- some creditors do it if you over pay too. I overpaid Kohls by $0.29 and they took it. They zeroed out the balance and the statement was $0 balance and the credit that should be there of $0.29 written off.
I don't think they should be able to do it when it's a credit, but perhaps they can. Or maybe its just rare enough and small enough no one has ever said anything.
other than loosing your penny, it shouldn't effect you.