Note: I have tried closing and rebooting Chrome (Version 54.0.2840.71 m (64-bit)) and have also removed and reinstalled the Paperpile extension. Zoom setting is at 100% in the browser window. This has been occurring on every PDF I’ve opened for the past couple of weeks.
Thank you for reporting this. It appears that the recent Chrome update has affected the code we use to identify the highlighted area. We are working on a fix.
We apologize for the inconvenience in the meantime.