Recently I made a git repo out of directory that already contained two git repo subdirectories. Since then I’ve only been committing at the parent level…
Today I broke by codebase and tried to rollback. But the rollback didn’t take for the sub-repos. I looked in github, and instead of directories, they had different icons: (See the bottom two)

What is going on? what are these icons? Has the parent repo been ignoring these directories? Is that default behavior with nested repos?
That’s not how git works. Each repository is its own repository and has its own state. You can link two repositories together by using submodules. The green arrow on a folder means that it’s a link to another repository (a submodule).
You can read more about git submodules here. Your post as it currently stands isn’t really asking a question.