When I go to add the note to the verse by selecting John 1:1 from the menu it selecting both the verse and the heading "I. Prologue" and the sub-heading "Chapter 1" . There does not seem to be any way to remove that highlighting from the headings. Just to be sure this was not just an anomaly on John 1:1 I went to Matt 1:1 and tried to add a note to verse 1 just to see what would happen.
I right clicked on verse 1 and when the window opened I selected Matthew 1:1 and then "Add note to Study Notes on John". Just as it did in John it highlighted the entire verse but it also highlighted "I. Infancy Narrative"
and "Chapter 1" as well.
When I add a note to a verse I want the note indicator to go on the verse I am adding the note for and not on the book section heading. Note that I am doing this inside the NABRE. I haven't tried it in other Bible versions to see if it is doing the same thing there.