That would make sense.
When I used to take a school bus, paid by the school, it was because I live a long distance from the school that would be impossible to walk to and from. (I lived in a very rural part of the country side at the time, and walking to and from school would be anywhere from a 4-5 hour walk)
My brothers and I were given a BusCard, which was inspected on pick up so the bus driver knew to take us.
He didn't however check when we got on the bus at the end of the day.
He probably should have though. I think it was because he was lazy and didn't want to make everyone wait and form queue's in order to get on, simply because there would be a lot of people in a small area in the bus parking area.
I guess the reason he would inspect on the way to though, is because he would obviously park up outside your house (In my case) or in the small villages, so it was easy to get everyones Cards.
Probably just lazy bus drivers. I know how un-enthusiastic they can be about their jobs, as well as how pissed off they can be. I'd be pissed off if I had to drive the richardheads in the bus I used to take, twice a day, 5 days a week and for a large majority of the year.
It was bad enough just sharing the bus with them.
Here's hoping you don't get the same problem again though. If you do, go to your school and complain to them. I'm sure that if you take a bus because you can't get home any other way, they legally have to get you back home, and it's their responsibility to do so. If the bus driver is stopping you from getting back, they'll have to do something. Whether that's stricter control of the busses passengers or different drivers, you'll defintely stop encountering the problem if you complain.