When you applied as a couple you probably nominated one person to receive the child tax credits (CTC). That's usually the same person who receives the child benefit. You should be able to check with HMRC which bank account the payment went into.
When you told them you left they would have stopped the joint claim from the date you said you were no longer a couple. A payment may have already been sent out, hence the overpayment.
You would no longer be entitled to CTC as a couple from that date BUT you may be entitled to the CTC as a single parent (�96 a week or so for two children). This could be backdated to the date you left and may sort out any overpayment.
Your local CAB can help you with this.