The bank, which is part of Lloyds Banking Group, said that the incident had affected a "small number" of UK customers, who will all be reimbursed.
A spokesman said that while the problem had been nationwide, it had only impacted parts of its network.
"We have had an issue where a small number of customers who have used these payment terminals have been double charged for their purchases," he stated.
However, the Bank of Scotland representative added that the issue has been fixed and that all customers affected will receive refunds by today (July 29th) at the latest.
In related news, some Barclays customers were unable to access their online banking services on Monday (July 27th), as a high volume of demand resulted in the bank experiencing "technical problems" with its website.