Botched Clipper card upgrade creates new problems for riders, transit agencies

Commuters returning to Muni after the holidays were frustrated to discover that their monthly passes through Clipper weren’t working Monday, in the latest debacle with the revamped transit card.

A separate Clipper malfunction prevented BART and Caltrain from collecting new fares that went into effect on New Year’s Day. Instead, riders on the two train systems paid last year’s lower rates.

They are the latest snags since an updated system — Clipper 2.0 — debuted last month after years of delay. And transit officials warn that the stress could last weeks…

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