Is the missing payment using a payment type of cash by chance? 

The most common reason for an AP entry to miss the bank module is that the payment code has a payment type of 'other' and this brings up an 'other account' field in the payment entry window.  If the user enters a GL account in that field it overrides the bank code and skips the bank module (even if the account number is the bank account).  To make sure the entry gets to the bank module, leave this field blank (unless you do want the entry to go to a different gl account than the bank code specified in the batch header). 

I have made this error by filling in the bank account in the 'Other Account' field. What is the best way to correct this so that the bank reconciliation can be completed?

Do a bank entry as a withdrawal for the amount of the payment and code this bank entry to the bank account gl.  This will result in a debit and credit to the bank account for no net change in the GL.  But will give you an entry in bank rec to clear.