A computer upgrade shut down BART

There isn't much different about bart. Slightly wider wheel spacing and such are things anyone making trains can handle.

the real problem is thinking they are different or that they need to innovate. Trains are common and they need not innovation but minor improvements over time.

I've heard that makes procurement way more difficult, you can't just order a train car in the standard gauge from many manufacturers. It's like big and tall sizing, yes, any place can make it, but there just isn't that large volume to create a liquid market.

But is this a problem that can account of the day-to-day difficulties of managing and using BART? Yes, procuring new train cars is more difficult (and likely more expensive), but BART has lots of other problems to tackle.

The problem isn't just the rolling stock. Everything in BART is at least somewhat custom including control systems and software. Very little can be shared with public transit systems in other metro areas so there are no economies of scale. Thus BART has to do a lot in house or depend on a limited set of specialized vendors at great expense.

If you had to buy a special car to be allowed to drive on Bay Area roads because they weren't the same as the roads in Chicago or Boston then a Honda Civic would cost $1M.

  There isn't much different about bart.

Basically everything on BART is unique to BART. Odd loading gauge. Odd track gauge. Lightweight aluminum chassis so none of the aerial infrastructure is designed to carry a heavier, more traditional car. Multi-part wheels with aluminum hubs to make extra noise. Non-standard traction voltage so BART struggled mightily to find replacement thyristors for the old cars. BART still struggles to keep their electric substations running. The original signaling system makes some sense, but trying to replace it with another NIH product in the 90s made zero sense. The original trains had glass with compound curves and BART could not find a vendor who could reliably recreate them. The current trains indicate ADA seating with the color green, reserving blue for the regular seats.

If it can be made differently or done differently BART will absolutely try to do so.

  the real problem is thinking they are different or that they need to innovate. 

Yep NIH is a huge problem for BART.

  then a Honda Civic would cost $1M.

For $1M you could build a single San Francisco Cable Car. Plus it's built locally.

Or intentionally designed by the original contractors for lock-in, like an Apple product or a John Deere tractor.

A cable car is a lot simpler than a civic - the complex parts are in the engine house elsewhere. the cable car is bigger but it has no engine, transmission and other such parts