Tri-Rail question (paying)

I have been using the Tri-Rail on and off for the last week (like 3 times total). I loaded up my card and tapped it before going onto the Train.

I usually watch and observe other people, wondering what they are doing. I dont see them tapping those machines, then the signs on the train 'tap when you leave' or the 'dont get thrown off...'

What is the rule of thumb with this public transportation? Do they get updated?

I bought a bus ticket too, but still had to pay $.50 more to cover the shift? Cant they update the computers for the right price?