Here’s a screenshot of highlights, a single comment, and also a bunch of squares that show up next to the highlights when I open the PDF in preview (after editing it in the beta editor):
Looked for a thread about this to comment in but couldn’t find one.
Those squares are actually comment boxes and are an artifact of the odd way in which Preview handles comments on highlights. We currently have to write in these comment boxes for every highlight to ensure that the ones with comments actually work. We are looking into ways to avoid this, but at the moment this is the compromise we have reached w.r.t. Preview and its non-standard implementation.