WEll, after 50 mins on hold, I got through to someone. Yes, the issue was that the balance on my transportation flex card went too low and it declined the transaction. I added a second (regular) credit card to the account so they can try billing that in the future if the main card is declined.

My account status is now ACTIVE but they said the card won't work until Friday. I remember it taking 2 business days for all changes to start working in the turnstiles and on the bus for some reason.