Did you run your September CharlieTicket through the brand spanking new Assembly Square station’s shiny turnstiles today, only to have your card rejected?

You weren’t the only one. CharlieTickets purchased through the MBTA’s Corporate Pass program didn’t work today (at Assembly Square and all the other subway stations), making for many frustrated commuters this morning. (Not like driving in was any better this morning ... )

Blame the company that made the CharlieTickets distributed through the MBTA’s corporate pass program, says MBTA spokesman Joe Pesaturo.

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“The firm that makes these specific passes failed to properly encrypt them with the code necessary to access the subway,” Pesaturo told Boston.com. “It’s unclear, at this time, how or why this happened. The MBTA is talking with the ticket-maker about the situation, and how best to rectify it.”

That ticket-maker, Electronic Data Magnetics, did not respond to a request for comment.

The good news is that only the CharlieTickets distributed through the Corporate Pass Program were affected (UPDATE: Pesaturo told Boston.com that a “very small number” of Semester Passes made by EDM were also affected). CharlieCards and tickets purchased through the vending machines should work properly.

If you have one of the affected CharlieTickets, your morning commute might have been a bit frustrating, but this evening should be much smoother. The Boston Globe reports that station employees will wave people with the bad tickets through and that EDM has already started distributing new, working tickets.

UPDATE: The Charles River Transportation Management Association released an email from the MBTA providing further details on the flawed cards. It estimates about 33,000 corporate pass users with the commuter rail pass are not working. After 3 p.m. today, customers with one of the bad cards can get new, working monthly passes at the CharlieCard store at Downtown Crossing or ticket offices at North Station, South Station, and Back Bay.