Some payments that should have been processed within two hours have taken nearly two days owing to a backlog following a system failure.
Bank customers have been pushed into overdrafts owing to the fault in the Faster Payments system used by most of the UK's banks and building societies.
The shutdown and subsequent hangover means some payments and transfers from Sunday afternoon have not yet cleared.
The operator of the service apologised and said any charges would be refunded.
The UK's Faster Payments system is one of the major pillars of the UK's infrastructure for moving money.
Payments, and transfers between bank accounts, using the system should reach their destination within two hours, and often clear instantaneously.
A fault occurred between 13:00 and 17:30 BST on Sunday, at a time when a total of 769,480 payments were being processed.
An estimated 1% of these - about 7,694 - are still outstanding nearly two days later.
Among them is the transfer of £3,000 that Jonny Evans, of Chorley, made from his savings account to his day-to-day current account after buying a Kia car.
The 37-year-old said the transfer was made on Sunday but had not arrived. He said he was "in no-man's land" and was paying an overdraft charge as a result.
"I often transfer money between these two accounts and it usually happens straight away. It seems this one went during the time zone of the fault, so I now have an overdraft charge," he said.
"It is annoying, especially just before holiday time. It isn't an easy thing to solve. I've had to leave work early to get to the bank and make long telephone calls to them. When something goes wrong like this, it always takes a while [to sort out]."
A spokesman for the Faster Payments service said that nobody should be left out of pocket as a result of the fault and the backlog.
He said that people in a similar situation to Mr Evans should contact the bank that has issued any charges to ensure they are refunded.
The spokesman said that the backlog had been created by some payments being rejected during the shutdown.
These payments were being checked manually to ensure that there would not be a double payment if they were resubmitted to the system.
"We would like to sincerely apologise to all affected customers - we are working hard with our technology supplier Vocalink and all of our participating institutions to ensure the outstanding payments are processed as quickly as possible," he said.
"No one who has been affected by this issue will be left out of pocket - the industry has a collective agreement to make sure customers are protected financially in situations like this.
"An investigation into the cause has started but, together with our infrastructure supplier, we are prioritising work to process the outstanding payments."