Nationwide customers have had debit purchases taken twice, sending some of them overdrawn, in the latest technical hitch at a financial institution.
The problem was caused by "human error" and meant some customers who used their Visa cards on Tuesday had duplicate payments also taken out on Wednesday, Nationwide said.
The building society, whose catchphrase is "On your side", recently benefited from a surge in activity from customers looking to switch accounts following NatWest's IT meltdown and Barclays' Libor-fixing scandal.
It apologised to customers and said the transactions will be corrected overnight tonight and any charges incurred as a result of the problems will be repaid "in full".
A Visa spokeswoman said there was no problem with Visa cards and all of its systems have been and are working correctly.
A Nationwide spokeswoman could not say how many of the society's four million current account holders were affected and whether every customer who used their card in the period will have had duplicated payments.
She described the mistake as a "one off incident down to human error".
Leigh O'Riordan said that he had paid for his annual rail season ticket from Billericay in Essex to London, at a cost of £3,422, but he found the payment had been taken out twice.
"In my case, this means I now do not have access to my money," he told the BBC website.
"It took me a while to get through to Nationwide, but they were very good and they apologised."
Alfrey Johns, from the Isle of Sheppey in Kent, told the Guardian website she only found out about the double debit when her payment card was rejected by a store. She said she had called Nationwide and was told about the problems.
She told the website: "I have been humiliated in the shop because my card was refused as the double payments have sent me overdrawn.
"I've been told that I won't be charged any penalties but to say I'm furious doesn't cover it."
The blunder will come as a blow to a building society which has successfully marked itself out as offering something different from the big banks.
Nationwide said earlier this month that it had seen a 45% increase in people transferring their main account to the society, including branch, online and telephone applications.
However the problems for Nationwide customers appear to be being resolved more quickly than those faced by customers of the Royal Bank of Scotland (RBS) Group.
Some Ulster Bank customers were left without their accounts being updated properly for a month after the IT chaos which also hit RBS and NatWest customers.
Nationwide customers also vented their anger on the society's Twitter account, which said in response to queries: "An issue with debit cards is affecting some customers. Sorry, accounts will be corrected ASAP."
One customer wrote: "£nationwide have had a problem with visa transactions. Everything I bought yesterday has gone through twice!!!"
Another said: "Anything that went out on the 24th also went out on 25th! Glad it was dog food & not mortgage!"
Nationwide said in a statement that any charges related to the problems caused will be refunded.
It said: "We have identified an issue where some current account card transactions made on July 24 were duplicated on July 25.
"This is a one off isolated incident and is down to human error. The duplicated transactions will be corrected overnight.
"We would like to apologise for the inconvenience this has caused and we can assure customers that should they incur any related charges these will be refunded in full."
Richard Lloyd, executive director of consumer body Which? said: "This again raises wider questions about how robust banks' systems and safeguards are as consumers bear the brunt of yet another banking glitch.
"The least Nationwide can do is keep their customers properly informed on the issue and we think they should compensate those people who have been seriously affected."
Nationwide later said that 704,426 accounts have been affected, of which fewer than 50,000 are thought to have been adversely impacted, by wrongly incurring charges or fees.
The building society emphasised that everyone will be reimbursed.