PDF document with notes has yellow squares, can't remove them
Here is how you can remove the notes from the linked document.


Open the linked document in Preview.
control click on the note icon and select Delete Annotation.


Or:


Open the linked document in Preview.
Click the note icon, which opens the note.
Press the esc key to dismiss the note but leave the note icon highlighted.
Press the delete key.


Or:


Open the linked document in Preview.
Click: Preview > Tools > Show Inspector
Click: Annotations Inspector
Click the Type column, so all the notes are at the top.
Select all the notes, then press the delete key.




I've uploaded a modified copy of the linked document here.