I wish I could help you out.
When I want to be sure that my kids will go back home, I hit "go back home" once their school activity starts. If there's no bus in your town, maybe they can go back by bike as soon as the school finishes.
I'd also suggest checking whether Nraas Traffic would help. I used that mod once for dealing with limousines, maybe there's an option for school buses.I've just read the site and there was nothing about school buses. On the other hand, if you have the module Career for Story Progression, you can disable carpooling. Perhaps, if you had disabled that, it's affecting your current household.