What I really don't understand about OneNote is the default to a white-board-like free form placement mode for text blocks. If you move it a little, accidentally, it's not aligned the same as the other notes.
This really put me off when I first started using it, and at a client site, it's really the only option. Otherwise, the organization system is something I've come to like/live-with, but still -- why the boxes that can be moved around? Is there a "turn off free-form placement" mode that I haven't found?