Bad naming of category "Chord"/"Note" in the Inspector
If one wants to make a note smaller, the intuitive thing to do would be to click on "Small" under "Note" in the Inspector. That, however only affects the notehead; if one wants the entire note to be smaller, one has to click on "small" under the "Chord" heading. This is all fairly unintuitive.
Likewise, coloring, hiding and selecting in most cases only applies to the notehead, not the entire note.