The unidentified defendant was allowed bail at Canterbury crown court in Kent on Friday but was not freed until Monday because it was not clear whether his bail surety had been paid.
But a defendant in an unrelated case at Westminster magistrates court in London on the same day was freed after a judge made allowances.
The software failure at RBS and two of its subsidiaries, NatWest and Ulster Bank, has affected 17 million customers. The banks are extending opening hours all week in an attempt to clear the backlog of problems and arranged for customers to be advanced cash when they have missed payments and had no available funds.
The banks face complaints from those who have incurred extra costs because of the computer problem.
HM Courts and Tribunals Service said: "Defendants are released on bail once confirmation of the receipt of bail is received.
"We are aware of only two cases where there was a banking issue. We were advised of one case by barristers yesterday morning.
"It related to a case last Friday and court staff used their discretion to ensure that the defendant was released as soon as possible. In the second case the judge made a judicial decision last Friday to release the defendant given the circumstances."
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