Ever accidentally run git add --all when you didn’t mean to add all your changed file to staging? I’ve done this many times especially because I use Oh My ZSH’s git alias which happens to be ga for git add and gaa for git add --all. Which makes it sometimes more error prone to stage all changed files.
If you’ve accidentally staged all your changed files you can unstage them all by using git reset.
This should put you back in the state you were before staging all your changes files. Allowing you to stage changed files individually before you commit.