The Clipper card is a pre-loaded fare card that works on five Bay Area transit agencies, eliminating the need for coins or multiple passes for riders who use more than one system.
It was first called TransLink, but it is now Clipper and since last year, use has exploded from 27,000 boardings a day to 93,000.
With growth have come problems.
"At Muni Diaries the submissions we receive are usually funny stories about the bus, but in the last two months, I would say, 25 percent are about Clipper cards," Muni Diaries editor Eugenia Chien said.
Muni Diaries helped ABC7 reach Denise Cho, who posted her story about being charged for what should have been a free transfer on Muni. She caught it on her Clipper account statement and called customer service.
"She said she would submit it to her higher-ups and then I may or may not hear within 21 days later about my refund pending investigation," she said.
The MTC says it's aware of a problem with the clocks on card readers in buses and is working to figure out how widespread the problem might be.
Three of the five agencies in the Clipper system have buses.
"As part of a system upgrade to the clocks, we have found electrical shorts in some of them, so the clocks are running too fast or too slow," John Goodwin from MTC said.
Another common problem is card readers not working at all, but operators still demanded fare from unprepared Clipper card holders. Muni Diaries contacted the MTA, which then told operators to treat a malfunctioning card reader like a broken fare box and let the Clipper card rider board without paying cash.
The MTC says most Clipper transactions go smoothly, but it is hoping to correct a variety of problems within the next 30 days.