FINRA said that Merrill Lynch has provided $32m in remediation, plus interest, to the affected customers.
The regulator found that from April 2003 to December 2011, Merrill Lynch failed to have an adequate supervisory system to ensure that customers in certain investment advisory programs were billed in accordance with contract and disclosure documents.
According to FINRA, the firm overcharged nearly 95,000 customer accounts fees.
The regulator also said from July 2006 to November 2010 Merrill Lynch failed to provide timely trade confirmations to customers due to computer programming errors that led to a failure to send customers trade confirmations for over 10.6 million trades in more than 230,000 customer accounts.
Merrill Lynch failed to properly identify whether it acted as an agent or principal on trade confirmations and account statements relating to at least 7.5 million mutual fund purchase transactions.