The man was granted bail on Friday at Canterbury Crown Court, but he was not freed until Monday.
In a second case, a defendant was freed when the court made allowances for the problem.
Millions of RBS bank accounts have been disrupted, due to what the bank has put down to a software change.
The glitch meant money was not transferred into or out of accounts, but while the problem has been fixed, a huge backlog of transactions remain.
NatWest and Ulster Banks, owned by RBS, have also been affected.
RBS boss Stephen Hester said it would take a few days for everything to iron out.
Hester said: “It shouldn’t have happened and we are very sorry.
“There was a software change which didn’t go right and although that itself was put right quickly, there then was a big backlog of things that had to be reprocessed in sequence, which is why on Thursday and Friday customers experienced difficulty which we are well on the way to fixing.”
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 [on Monday]. 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.”
RBS is to change its working hours to 8am-6pm, at 1200 main branches this week to help clear the backlog of work.
It has promised to reimburse customers left out of pocket.
“We will automatically waive any overdraft fees or charges on current accounts,” said Susan Allen, director of customer services at RBS.
“This will be processed over the next few days,” she added.
The bank says its own customers who have suffered financial losses should take their case to a local branch where managers will arrange to pay them back. Claims are being judged case by case. Customers are advised to take documentation to back up their stories.