I agree, it is really annoying if that happens.
Most Halifax current accounts will allow you a free overdraft facility, which would prevent this from happening, but I think you have to request it, so it might be worth asking if your account has it.
I very rarely write cheques nowadays, as it is harder to keep track of your balance, as they can be drawn on your account anytime, up to three months after writing them.
As other people have said, go in and speak to someone, explain what happened, and there is a good chance they will cancel the fee.
Good luck.