In July the banks revealed they had miscalculated 18,000 mortgages and suggested customers make up the shortfall.
But FOS revealed a surge in complaints following the error and has now upheld some complaints by customers who appealed against the banks’ decision.
A spokesman for Clydesdale Bank says: “We continue to review each case on its own merits and seek to help customers based on their individual circumstances.
“The vast majority of customers have accepted this was a genuine error and they are simply being asked to pay back the amount they had originally agreed when taking out their mortgage.
“To date a relatively small number have referred their complaint to the Ombudsman, where their case would again be reviewed on their own merits. We can confirm that in some cases the Ombudsman has found in the customer’s favour.”
The banks were forced to apologise to the affected variable rate customers in July after miscalculating monthly payments.
Some customers were paying less than the minimum, so many now have shortfalls on their mortgages and are not on course to pay off their loans within the agreed term.