Some duplicate mortgage payments were mistakenly taken from customers during NatWest's IT meltdown, the bank's group has confirmed.
Royal Bank of Scotland (RBS) Group issued the latest in a series of apologies to customers and urged them to get in touch so it can put the problems right.
The group said it believes a "small number" of customers have been affected and promised that no one will be left permanently out of pocket.
A spokeswoman for RBS Group said: "We apologise to any customers experiencing problems today. We said last week that we expected to see a few bumps in the road for customers as we get things fully back on track.
"Any customers experiencing problems should contact our call centre or visit their local branch and we will put things right."
The group has been working "round the clock" to resolve the problems which began two weeks ago and meant NatWest, Ulster Bank and RBS customers' balances were not updating properly.
It has had greater difficulty clearing up the glitches, which meant people's wages did not appear and house purchases and holidays were disrupted, for Ulster Bank customers.
RBS Group chief executive Stephen Hester said last week that he will forgo his bonus this year because of the chaos and has promised a "full and detailed investigation".
Despite facing some calls to quit, he has said he is determined to "personally lead the process" of regaining customers' trust.
The banking group's initial findings were that the problems were created when maintenance on its systems, which are managed and operated by its team in Edinburgh, created an error which stopped people's accounts updating properly.
The problem was made worse because the team could not access a record of the transactions that had been processed up to the point of failure.
A "substantial backlog" was created because the group, which processes 20 million transactions a day, had to try to pinpoint the moment at which processing had stopped, which created more delays.
The bank boss said on Friday that, while a "large number" of customers' problems had been resolved through bank branches and call centres, around 15,000 required a greater degree of attention.
While the banking group has said no-one will be left permanently out of pocket and has urged people to keep records of how they were affected, many customers have argued they should be given compensation for their inconvenience on top of their losses.
Fears have also been raised that customers could unwittingly have their credit ratings blotted, although the bank is working with other agencies to make sure this does not happen.
RBS Group extended its opening hours to cope with the chaos and even took the step of opening on a Sunday for the first time.
Mr Hester has previously been forced to waive his £963,000 all-shares bonus amid public outrage over bankers' pay.
RBS paid £785 million in bonuses last year, including £390 million for its 17,000 investment bankers. While the total pot is 43% lower than the previous year, it followed a period in which the bank announced thousands of job cuts.
The beleaguered banking group had to scrap its corporate hospitality at Wimbledon as it grappled with the problems.
Some customers writing on NatWest's website today said they were still experiencing problems with money showing up in their accounts.
In a reference to Barclays chief executive Bob Diamond, who has fallen on his sword following the rate-rigging scandal, "Skint from Bradford" wrote on the "ideas" section of NatWest's website: "Mr Diamond has resigned - will you do the same Mr Hester?"
Ulster Bank has said that it has made "steady inroads" to its delays, but added that while the pace of progress has improved it has been slower than customers would have liked.
Ulster Bank customers should hopefully see their balances updating over the coming week, the bank's parent group has said.
Due to the way the technology was set up when the three banks were integrated, Ulster Bank payments happen to follow in sequence after those of NatWest and RBS, which "in no way" reflects any priority given to customers, RBS Group has said.
Analysts have said that people's decisions on whether to switch accounts could hinge on how satisfied customers are with how the banking group puts the problems right.
However, building society Nationwide said today that it has seen an 85% increase week-on-week in the number of customers opening and transferring their main account online.
Including customers who have switched their accounts in branch as well as online, the society said it has seen an overall rise week-on-week of 26%.
John Crossley, Nationwide head of current accounts, said: "Customers are clearly unhappy with recent events and are opting to vote with their feet."