This sounds very strange of your bank. Where I come from, you have to sign a document to allow overdraft to occur, otherwise a withdrawal or transfer request will simply be turned down or a cheque will bounce. What you said earlier made me think that you have an overdraft facility allowed.
First off if it's without your knowledge and permission, then you did no wrong. I apologize if I misunderstood earlier. Whatever is charged by the bank if it cannot be argued to be waived, you can just pay it to cut their pain.
Second, I advise you to either get their procedural adjustment to not allow any overdrafting, or change your bank if they won't do that. It happens regularly that people don't know what's remaining in their account so it's bound to happen to you and me that we ask for a withdrawal at an ATM or something without having enough at that time (forgot about an earlier payment, had the money in a different account etc.) so leaving it open like that subjects you first to unnecessary costs and puts you in riba. Try to change the situation.
But anyway, if it happened without your knowledge and intention, don't worry. God does not bear what we do not know of and accidental mistakes and things we forgot: "[FONT=Verdana,arial]On no soul doth Allah Place a burden greater than it can bear. It gets every good that it earns, and it suffers every ill that it earns. (Pray..) "Our Lord! Condemn us not if we forget or fall into error; our Lord..." [2:286] [/FONT]