The problem is that you're still marked as having entered the system, but never exited. So the turnstiles won't let you in next time you try to enter a station, as I understand it.

The proper SF solution, based on my observations, is to just jump the turnstiles every time, going in or going out. I've watched guys camped out on the floor shooting up in clear view of the attendant, I assume if that flies they probably won't chase you down for just jumping a turnstile. (Yes, I do pay every time I ride BART, and yes I have been bitten by this stupid goddamn charge, and no there wasn't any attendant at the station to fix it)