The firm sent an email which read, "Twitter believes that your account may have been compromised by a website or service not associated with Twitter," then reset the passwords of numerous accounts.
Twitter said that in situations where they believe an account has been compromised, they reset the password and send an email letting the owner know they've been compromised. Twitter users who received the email were prompted to create a new password.
"We unintentionally reset passwords of a large number of accounts, beyond those that we believed to have been compromised," said Twitter in a blog post.
Twitter explained that what they did is a "routine part of our processes to protect our users."
"We apologize for any inconvenience or confusion this may have caused," said the company.
Twitter is no stranger in being a target for hackers or fake accounts.
A study by Barracuda labs this year revealed they had found at least 11,283 'abusers' with over 72,000 fake accounts.
The average abuser was found to have 48,885 followers and the average fake twitter account was following at least 1,799 accounts.
The study also found that over 60% of fake accounts are less than three months old with the average age being 19 weeks. The oldest fake account dates as far back as January 2007.
"Creating fake Twitter accounts and buying/selling followers is against Twitter's ToS, and gradually erodes the overall value of the social network," said Barracuda Labs.