I don't know what to tell you, except that when I viewed the page, there was a reasonably well-formatted PDF in the center of the screen surrounded by unnecessary, fiddly, bouncing bullshit "click on me!" buttons.
I think these are simply the paper annotations. It's not that obtrusive.
There are sites that allow for annotations and manage to do so without bouncing, distracting "click on me!" buttons. Medium does a great job of this. I have no idea what the site's creator was thinking when they decided not to emulate the established, non-distracting examples instead of doing what they did.