About a year ago Caltrain took away conductor discretion when issuing fare evasion citations ordering them to write up violators and let a judge decide whether it was right or wrong. It was criticized at the time as draconian by some but Caltrain said it was necessary since they had a barrier free system. And also that enough time had passed for people to become familiar with using Clipper. Discretion though meant the conductor could decide on their own whether writing a ticket was actually needed. Perhaps it was someone new to the system or got the wrong ticket. If they see the person a lot on the train, it might just be a one time thing and get a warning. The fare evasion ticket is $300 plus whatever court fees or other fees that may be imposed.

That policy appears to be over. In the fall 2013 edition of
Caltrain Connection, an official publication of Caltrain, in the question and answer section about fare evasion tickets is this:

Q: On two separate occasions I’ve been on Caltrain and
have witnessed two conductors not issuing citations to
riders that did not have proof of payment. Why do some
people get warnings while others get citations?

A: Conductors have the authority to issue a citation to
any customer without a valid fare. However, they also are
allowed to use discretion when issuing citations depending
on the circumstances. As a barrier-free transit system,
it’s important to check fares and issue citations as
needed.

One wonders whether someone over at the court dropped them a line about all the citations showing up from Caltrain. Or simply wiser heads prevailed. At any rate, giving the conductors back the discretion is a good thing. They can usually discern if it is an honest mistake or someone trying to get a free ride.