The system was shut down between midnight and about 7:15 a.m. Some people on the last trains of the night were trapped inside those trains for two hours. Some passengers arrived very late at the Pittsburg station at 4 a.m.
BART rider Robert Freeney said, "I am furious and this is ridiculous. I'm through with BART. I'm done."
BART rider Antoine Lax shared with ABC7 News how he felt at 4 a.m. He said, "Right now, I'm extremely tired and a little irritated too at the same time."
BART says it was a computer problem stemming from a software upgrade done earlier Thursday and it took seven hours to figure that out.
"Information between servers that is usually exchanged wasn't happening and that impacts computer systems used by the operations control center to monitor trains," said BART communications director Alicia Trost.
The stuck trains could be moved forward, but only slowly and switching tracks had to be done manually with a crank.
"Every time you pass over what's called a crossover, the track that determines which way it's going to go, someone had to go out and manually move it to make sure it was heading in the right direction and that just takes time," said Trost.
The shutdown meant horrible traffic on the freeways and long waits on the BART platforms for early morning commuters still hoping to grab a train into work.
"We got people who have been standing here, myself for two hours, and other people were here before me," said BART rider Ward Kalinowski.
"They need better management, different people on the board, I can't say anything about the unions because I don't know a lot, but whoever's running this, needs to sit down, throw out the plans that they have and start over," said BART rider Cynthia Patrick.
BART says there was no sign of any deliberate tampering with the computer system. It was just a technology failure.
BART provided free parking at all of its stations for the day to apologize for the shutdown.
BART spokeswoman Alicia Trost issued the following statement:
"Yesterday BART implemented a planned infrastructure upgrade to a network server. 12 hours later this change began to impact the exchange of information between servers, which affected the performance of the computer system the Operations Control Center relies on to monitor train service. Eventually the central computer went off line, which caused the last trains of the night to be delayed upwards of 2 hours due to the need for Train Operators and maintenance crews to manually move and lock switches.
ABC7 News reporter Amy Hollyfield contributed to this report.