If it's so easy to do better, I suspect an alternative (that works for people without smart phones) would have been mentioned in the post.

As it stands, it's just a matter of riders developing the tap-out habit.

Transit systems elsewhere have used this system. If you'd never become used to the old more casual system, you'd just always know to both tap-in, and remember to tap-out, or you'll be overcharged. If you'd been more used to, say, BART than CalTrain you'd also be better primed for the Clipper system: it works like the BART turnstiles, only without the clear physical barrier/reminder.