"The crowdsourced, more criminal investigation was very volatile and fraught with problems, and, obviously, wrong," Reddit general manager Erik Martin told CNN. "That was something we all wished hadn't happened."
The moderator of a subreddit, or comment thread titled findbostonbombers, which had been set up to crowdsource the identities of the bombers, also apologized, the channel said.
One group of redditors, as the site's users are known, had speculated that Sunil Tripathi, a Brown University student who has been missing since last month, could be a possible suspect. Tripathi's family temporarily took down a Facebook page asking for help finding him after they were bombarded by ugly comments.
Other Reddit users focused on two young men with heavy-looking bags, one of whom wore a blue track suit.
The New York Post even splashed a photo of the two marathon spectators on its front page with the headline, "Bag Men: Feds seek these two pictured at Boston Marathon."
The guy in the track suit turned out to be a 17-year-old suburban Boston track star who told a news agency he was afraid to leave his house because of the scrutiny, CNN reported.
Critics too have posted scathing comments on the Reddit fiasco.
The Atlantic's Alexis Madrigal wrote a column called "Hey Reddit, Enough Boston Bombing Vigilantism," and followed it up with a story on how the names of two innocent people got repeated in a viral loop on social media.
Photos: Shraddha Kapoor, Kim Sharma at 'Haseena Parkar' screening
Mumbai to Goa train: First look at the glass-top Vistadome coach
Shuttler Ashwini Ponnappa keeps it short and sexy on social media
Photos: Narendra Modi, others at Marshal Arjan Singh's funeral
Photos: Sussanne Khan and Nimrat Kaur spotted at a spa in Juhu