One day before the Bay Area switched on Clipper 2.0, the Metropolitan Transportation Commission's own director of Clipper put his objection in writing: the system's central task — collecting fares and paying them out to the right transit agency — still wasn't running on autopilot. The commission launched anyway.

Internal emails obtained by KQED show the software failures that unraveled Clipper 2.0 after its late-2025 debut were no surprise — MTC and contractor Cubic Transportation Systems had traded blame over persistent errors for months. What the records lay bare is a decision: MTC leadership, racing to get the tap-to-pay upgrade into riders' hands before Super Bowl and World Cup crowds arrived, judged that shipping outweighed a risk its own staff had put in a formal letter. The gamble landed on a system 22 Bay Area operators depend on to move money, at the exact moment those agencies are asking voters to bail them out.

The day before launch, MTC Clipper director Jason Weinstein put a formal objection on the record, KQED reported (external source, opens in a new tab) after reviewing internal communications. He wrote that the commission could not be confident fares were being gathered and paid out to the correct operator — the software's core purpose — because too much of that work was still being done by hand rather than automatically, in a network that clears several hundred thousand transactions a day. Weinstein said MTC would hold Cubic to its contract. The tension, KQED found, ran back months: agency officials said the contractor could not stamp out recurring errors, while Cubic's staff said MTC had never authorized enough testing.

MTC Executive Director Andrew Fremier defended the timing to KQED. Commissioners, he said, wanted the tap-to-pay features working before Super Bowl and World Cup crowds flood the region's trains and buses, and with Cubic promising quick fixes, leadership decided the payoff outweighed the documented risk. No system is ever flawless, he argued, and the agency did not want caution to keep useful tools out of riders' hands.

The reporting is a KQED exclusive; The Dissent has not reviewed the internal emails. But the failures that followed are a matter of public record — and independently document how thin that reassurance turned out to be.

The most humiliating example came on May 18, when a 27-hour outage knocked out BART's ticket vending machines and jammed its fare gates. The cause was not a sophisticated software fault. An AT&T network circuit linking BART's data center to Cubic's system had gone dead because Cubic failed to pay the bill on one of several AT&T accounts — and, its own chief operating officer Lalit Singh conceded, the company had not even known the BART circuits lived on that account, KQED reported (external source, opens in a new tab). BART General Manager Robert Powers was incredulous that a missed bill could take the system down, telling the June 2 board meeting that the contractor had lost all credibility with the agency.

That outage was one entry in a long ledger. Cubic blew past its own May 30 target to begin the bulk migration of existing accounts to Clipper 2.0; nearly six months after the December launch, only about 1.7 million cards had been converted and just 45% of Clipper fares were being paid through new accounts, KQED reported (external source, opens in a new tab). In July, nine Bay Area transit operators — including the four largest — pressed MTC in writing to "pursue all contractual remedies" (external source, opens in a new tab) against Cubic. The company has run Clipper since 2009; in 2018, MTC approved the $461 million overhaul contract — a deal that keeps Cubic operating the system through 2032, the commission announced at the time (external source, opens in a new tab).

The timing is the sharpest part. Clipper 2.0 was supposed to be a rare win. Instead, BART, Muni, Caltrain and AC Transit are heading toward the November 2026 ballot with a regional sales-tax measure (external source, opens in a new tab) — one of two tax measures the agencies are counting on to close cumulative annual deficits projected near $900 million. Asking voters to trust agencies with new money is harder when the agencies' most visible tech upgrade takes riders' money without crediting their accounts.

SFMTA transportation director Julie Kirschbaum told a June meeting of the Clipper Executive Board that the reputational hit — on a project that was supposed to be a rare bright spot — was unacceptable, per KQED. Cubic's spokesperson, Cory Shields, called Clipper among the most complicated fare-payment networks in operation; the company did not answer KQED's questions.

In July, nine Bay Area transit operators — including the four largest — pressed MTC in writing to "pursue all contractual remedies" against Cubic.

The Dissent has tracked the drift for months — from the board that cancelled its June oversight meeting with no explanation, to autopay charges that kept hitting cancelled accounts. KQED's records add the piece that was missing: evidence that the people running Clipper saw the cracks before they widened, and hit go anyway.