Stubblefield's name and those of several of his Oakland Raiders team members were found on the list of clients of the Bay Area Laboratory Co-operative that had given performance-enhancing drugs to Marion Jones and others. Although initially he lied to federal investigators about using both EPO and THG, after he was charged on January 18, 2008, Stubblefield cooperated with both federal and NFL investigators and turned over the names of players, agents, and trainers that he suspected of using drugs.
Because of his cooperation with the investigation, he received a fairly light sentence after pleading guilty to lying to federal investigators on February 6, 2009. He served two years probation.
On October 12, 2010, former NFL agent Josh Luchs mentioned in an article for Sports Illustrated that he offered Stubblefield $10,000 cash while he was still playing football at the University of Kansas, but Stubblefield refused to accept it.
On December 9, 2010, San Francisco U.S. District Court judge Susan Illston sentenced Stubblefield to 90 days in jail for stealing his former girlfriend's mail by way of fraudulent submission of a change-of-address form.
On May 2, 2016, he was charged with sexually assaulting a disabled woman, who at the time of the incident, was 31 years old. The incident occurred April 9, 2015. Stubblefield originally contacted her through a babysitter website. Bail was set at $250,000.