Chief Joey East confirmed the incident Thursday, saying Henderson was cited for not having proof of insurance. He said no other charges were filed and Henderson was never arrested.
An Ole Miss spokesman declined comment. Kennedy did not immediately return a message seeking comment.
East said officers told him Henderson was "very cooperative" during the stop and "it's not uncommon" for police to find small amounts of a suspected controlled substance but file no charges because of a cooperative suspect.
The Wall Street Journal says police reports show Henderson was pulled over May 4 on suspicion of speeding. An officer smelled marijuana in Henderson's vehicle and Henderson handed the officer a bag with "a small nugget of marijuana." The report also says a search by a police dog found a clear plastic bag that contained "a small amount of what appeared to be cocaine."
According to the newspaper, the officer noted in the report that the district attorney wouldn't prosecute such a small amount of cocaine.
East said the suspected marijuana and cocaine were not tested and officers did not determine Henderson was under the influence of any drugs or alcohol.
"If they had suspected that, he would have been arrested," East said.
Henderson averaged 20.1 points per game last season, helping the Rebels advance to the NCAA tournament for the first time since 2002.
Henderson came to Ole Miss his fourth college with a history of discipline problems. He was arrested in 2009 for misdemeanor forgery after buying marijuana with counterfeit money and again in 2011 for misdemeanor possession of marijuana. He served time in jail after the second arrest because he violated his probation.
Ole Miss has said the coaches were aware of Henderson's past when he signed with the program.
It's not the first time Henderson has made headlines during this offseason.
He wrote a message in April for the university's website, thanking Ole Miss fans for their support and vaguely apologizing to "anyone I offended." The flamboyant guard rarely hesitated to needle opposing fans during one of his frequent scoring sprees.
He was also reprimanded by the NCAA in June for making an "inappropriate gesture" following the Rebels' loss to LaSalle in the third round of the NCAA tournament.
Now comes his most recent suspension, which puts his future with the program in doubt.
"Since the season ended, we have talked a lot about Marshall taking a greater leadership role with our team," Kennedy said in Wednesday's statement. "With that comes greater responsibility, and he must do a better job of living up to the high standard we expect from him and he desires from himself."