Before performing, Tank called on the crowd at the USC Galen Centre to stand in a show of respect for those who lost their lives in the terrorist attacks 15 years ago.
But Brown refused to get up, instead nodding his head and clapping at the end of the performance.
The Zero singer's act of defiance sparked outrage, with some Twitter users branding him a hypocrite.
Brown was later spoken to by police after getting into a heated exchange with a spectator in the stands, though loud music made it difficult to hear the nature of their row.
One of the officers at the event at USC's Galen Centre in Los Angeles could be heard saying in footage of the incident: "I don't care who's here, get it straight."
The news comes after Brown was arrested on suspicion of assault with a deadly weapon at his LA mansion last month when beauty queen Baylee Curran accused him of pointing a gun at her.
During an hours-long siege, Brown verbally attacked law enforcement officers.
In a series of Instagram videos, he accused police of "defacing" his character and making him out to be a villain.
