When items are missing from the Bank Reconciliation because of duplication, if monies have been paid into the wrong account you can choose a couple of options:
These monies can be posted to the matter that the duplication relates to, then when transferred back posted off the matter.
These funds if not relevant to any matter could be posted to a misc matter and then transferred through to the correct bank and posted correctly.
An adjustment can be done on the bank until potentially a matter is needing to be created if that is what is required for the money to go against.
If you have a posting that looks to be already reconciled then check what the original item was reconciled against and then check the matter numbers/nominal codes if these are the same or different.