The Virginia-based bank said in a tweet on Wednesday that its support teams are "engaged and working towards a fix" and reassured customers that they will not be responsible for fees related to the issue.
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The bank could not immediately provide an estimate for when the issue would be resolved.
Some customers claimed on Twitter that the issue was so severe that it left their accounts overdrawn. Customers affected by the issue do not need to report the charges, the bank said.
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While Capital One only addressed issues with debit card purchases, some customers said on Twitter that they were experiencing similar issues with savings accounts and credit card accounts.
The company cautioned that wait times for phone support are long and encouraged customers to connect with the company through online banking or its mobile app.