Muni riders across San Francisco can expect a more crowded commute on Thursday, as the railway runs about a dozen trains with just one car instead of the usual two.

The railway learned about a problem Wednesday with the pins that keep its new fleet of red-and-gray Siemens trains coupled together: They only last about three months before becoming unreliable. Known as shear pins, they are one of two ways railway cars are held together.

“There is no risk to riders because even if one of these (trains) uncouples, our brakes would stop a train from going anywhere,” said Erica Kato, spokeswoman with the San Francisco Transportation Municipal Transportation Agency.

But the railway is taking no chances. They are running trains with older pins as singles until the train manufacturer can rush out a stack of fresh pins at its expense.

Meanwhile, Kato said, Siemens will “re-design and re-engineer” the pins so Muni doesn’t have to constantly replace them on the 68 new trains it’s bought since last year to augment its older fleet of 148 Bredas and 60 historic streetcars. In all, the agency has ordered 260 of the new rail cars for $1.2 billion, with the next arrivals to begin in 2021.

The “pin fatigue” problem is just the latest headache involving the new cars, the last of which rolled out this month.

But it’s the second time this year, that the agency has had problems coupling the new train cars. In May, nearly a third of 104 couplers were found to have a defect of some kind.

A month earlier, a woman fell onto the tracks after a Muni train door closed on her hand. Since then the agency has added sensors that prevent the doors from closing on fingers.

The agency also had to fix the brakes to stop them from causing the trains’ wheels to flatten. And in 2020, Muni expects to replace the bench seats in the new trains because riders found them slippery and irritating. The new seats will be more bucket-shaped.

Kato said a train operator discovered the latest problem with the shear pins on Wednesday in the bus yard when she sensed that “the ride felt different.”

Not all trains have older pins, and Muni is spacing out the dozen or so single trains across the system to minimize the impact on riders.

“This is a very short-term problem,” Kato said. Thursday’s ride “might be a little more crowded.”

Nanette Asimov is a San Francisco Chronicle staff writer. Email: nasimov@sfchronicle.com Twitter: @NanetteAsimov