Discrepancies can be caused by one of the following reasons:
Reconciled transactions that were changed, deleted, or added after your last reconcile will affect the opening balance. There are several reports available in QuickBooks Desktop that will help you identify discrepancies and fix transactions.
Reconciliation Discrepancy Report: This report shows transactions sorted by statement date that were changed since the last reconciliation.
Missing Checks Report: This report helps you verify missing transactions.
Transaction Detail Report: This report helps you verify transactions that were changed or modified.
A forced previous reconciliation which resulted to reconciliation adjustment may also cause discrepancy. To fix this issue, you need to review the Reconciliation Discrepancy account for inappropriate adjustments. (You must have first reconciled the account and entered a Reconciliation Adjustment)