The shooting happened Monday night after the suspect was stopped for reckless driving in the Union City Station parking lot.
The 32-year-old woman was shot in the upper body. She is recovering at a local hospital and faces felony criminal charges once she is discharged.
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"These incidents are infrequent on BART. And they're investigated to our full capabilities. And we are very successful holding people accountable for crime and disorder on BART," said BART Police Chief Kevin Franklin.
Chief Franklin says the two officers involved had their body cameras activated.
The footage is now part of the investigation.