If you recall from a few years back, the Clipper card allowed BART passengers to enter the system with a minimum value on their card and exit the system with a negative balance. If the card was unregistered, the card can be easily thrown in the trash and the taxpayer takes the brunt for the lost money. Thanks to some news reporters exposing this problem, it exploded to the point where tens of thousands of dollars was being lost per month because people could cheat the system. I tried to help mitigate the problem by encouraging people not to cheat the system.
Back in September 2011, the MTC estimated the loss due to people dumping their Clipper cards with negative balances was $360,000 in lost fare revenue, and when combined with the cost to procure the Clipper cards, the grand total was $700,000 a year. It wasn't until June 2012 that the MTC had the guts to get the paperwork signed-off to get that loophole closed for the BART system.
The New Official Policy:
Over a year after the MTC approved the funding, BART made an announcement yesterday (September 30th) on their website. It basically says that starting October 5, 2013, passengers will not be able to exit the system with a negative balance on their Clipper card. Passengers with a card balance not enough to exit the system, will need to use an exitfare machine to add funds in order to be able to exit the system.
But there's a few catches with using the exitfare machines:
(1) You can only pay in cash to add additional funding to your card. No credit or debit cards.
(2) It will only top-off to the amount necessary to exit the system. That means once you paid the amount to the machine and exit BART, your card balance will be zero.
(3) The maximum amount of change the machine will return is $4.95. Only have a $20 and you owe BART a dollar? You just got screwed.
Two easy tips to avoiding the exitfare machines:
(1) If you have autoload (in which I personally do not recommend), you don't have to worry about using an exitfare machine because your card will automatically reload funds at a set tolerance limit.
(2) If you do not use autoload, keep an eye on your Clipper Card balance and make sure you add additional funds as necessary at any BART ticketing machine.