Every note-taking system is a map of what you know. Like any map, it leaves things out on purpose. That is what makes it useful, and also what makes it misleading.
Maps get stale
The world keeps changing after you write a note about it. A tidy system full of old notes can make you feel informed when you are not.
Keep the map small
I've found it helps to keep fewer, better notes, and to revisit them. A small map you actually look at beats a large one you don't.