Delays are affecting trains in both directions and the train that struck the debris had to be taken out of service. According to KCBS the obstruction was some loose sheet metal that ended up touching the electrified third rail:
BART major delays because of sheet metal on the tracks inside the transbay tube touching 3rd rail. http://t.co/xaxvbsQkwD— KCBS Traffic (@kcbstraffic) November 27, 2013
BART says the obstruction has been cleared and that the system is now recovering, but you can expect delays to remain for a little while longer this evening. In the meantime, we'll be sure to update once BART comes out with an excuse for what that loose sheet metal was doing in the Transbay Tube to begin with.