The bank had intended to simplify the system by asking people who intended to pay off the entire amount to pay on one cheque.
The cheque would then cancel the direct debit. If the cheque did not arrive the direct debit would be activated.
One client who has suffered because of the original change is Keith Tritton from Bedfordshire.
Six months ago he took out a Co-operative Bank Visa card choosing to pay off the minimum sum with a direct debit while paying the rest on a monthly basis with a cheque.
However, in October Mr Tritton's statement revealed that the direct debit had not been claimed, and as a result he was charged pounds 5.50 in interest.
When he phoned to complain he was told that because of a peculiarity of the computer, the arrival of a cheque triggered cancellation of the direct debit. The bank refunded him the interest.
The following month, the same thing happened again and he was charged pounds 2.57 in interest.
He said: 'I again phoned to complain, but this time was refused a refund on the grounds that I had been warned of this problem before.'
The bank said that it had introduced the new system so that people would not have to subtract the minimum amount from their cheques, but it accepted that a number of people had had problems.
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