The problem led many customers to believe that it was the stores who were at fault, and not the bank, retailers said.
Independent retailer Chris Parton was forced to make two refunds to appease angry customers in his Fort William store. "Some people came to the shop very angry about it because they thought it was us who had charged them twice," he said.
The Bank of Scotland confirmed that the problem had been UK-wide, but that it had not affected its whole network.
Bank of Scotland PDQ machines are used by more than 20,000 merchants across the UK.
One unlucky couple were charged twice for a £4,414 hotel bill, leaving them overdrawn.
A spokesman for the bank said the problem had now been resolved and that all affected customers would be reimbursed.