Millions of Nationwide customers could be left hundreds of pounds out of pocket, after a "human error" meant payments from Visa debit cards were duplicated.
The error sent many customers overdrawn and cards were stopped - causing outrage on social networking sites.
The Nationwide has around four million current account users, but the building society said those affected would only be Visa debit card holders who used their account on 24 July.
Leigh O'Riordan told the BBC 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 said.
A Nationwide spokeswoman said: "We have identified an issue where some current account card transactions made on 24 July were duplicated on 25 July. 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."
She said those who had gone overdrawn or had payments bounce should contact the bank to make sure any related charges were reimbursed. She denied reports that two million people had been affected, but said they were not clear yet as to how many were.
Many only became aware this morning after they found they could not use their cards. The accounts will be credited by the building society on Thursday night but have left many without funds until then.
A spokesman for Visa said all of its systems were in working order.
The Nationwide error follows the large scale disaster at Royal Bank of Scotland, which meant many Natwest customers could not use their accounts after an IT meltdown. Customers were missing wages and other payments, and missed bills.