BART police officers tackled the man to the ground and took him away in handcuffs.
"But there's real blood on the ground. There's real blood. BART has blood on their hands," said the protester.
No one was hurt, but Dugger had red paint on her hands and clothes.
Other protesters denounced the move, but continued on with their frustrations about the agency's handling of the New Year's Day shooting.
From the beginning, BART's board had lost control of their own meeting.
As they've done for months now, protesters called on BART police to give up their weapons, and demanded the resignations of Dugger and BART police Chief Gary Gee.
The confrontations were heated.
"That officer lynched Oscar Grant out there," said one protester.
"My Godson was like this take a look at it. Shot in the back and rolled over. And you want me not to be angry today?" said another protester.
Board member Tom Radulovich said the agency has heard protesters' demands, but some of them are out of the transit agency's control.
"We can't control what the courts do and it's to charge officer Pirone. BART can't charge anybody with anything," said Radulovich.
The man who threw the paint is 31-year-old Gabriel Meyers of Citrus Heights, near Sacramento. He's in custody in the alameda county jail and was booked on two counts of battery, one count of disturbing a lawful assembly and one count of resisting arrest.
Meanwhile, the investigation into grant's shooting continues.
The former BART officer, who shot Grant, Johannes Mehserle, has been charged with murder. He is out on bail and due back in court on May 18.