It's because we built a lot of the prisons at the same time we built a lot of the schools. They're both usually intended to serve multiple generations, and while the usage requirements may grow they don't grow so fast that you need to tear them down entirely and rebuild, usually just renovate.
They're also usually designed with more functional requirements to makes certain parts of them mandatory.
For example, schools often must have a certain amount of windowless hallway where the walls are a prescribed strength for tornado safety. Needs to be within a certain range of each classroom, have a limited amount of potential debris, and so on. As a result, every school ends up with at least one "hub" hallway that's fucking bleak as hell, because the storm shelter requirements also make it a very obvious hub to build classrooms off, and if you need to add more capacity: make the hall longer.

I've seen some designs where newer schools are being built with the shelter but as a + in the middle, with a windowed hallway around the outside, or even just taking the same floor plan and bending it to give classrooms larger window surfaces.