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BART Running Late

What causes BART trains to be late? I have noticed that on a fairly regular basis, the train from Bay Point to SFO gets held underground in Oakland (after leaving 12th Street) for what we are told by the TO is a late train from Fremont being given priority.

Some days it seems it only takes 30-60 seconds, but other days it takes 2 minutes (maybe a little more) for this simple transaction to take place. Doesn't this cause the SFO bound train to also be late now? I don't know, it is so hard to get the full truth from anyone at BART (it's run like a typical government bureaucracy), but it seems silly to sacrifice two trains, but like I said "it is so hard to get the full truth from anyone at BART.

One choke point for trains is

One choke point for trains is West Oakland station into the Transbay tube. The other one is at Embarcadero station coming out of the Transbay Tube. With 56+ trains running at the same time, it only takes a glitch like a door problem on one train to alter the schedules for lots of trains.

The printed schedule on BART is only a guideline.