I don't bother reporting 'bugs' anymore.  Just interesting new Logos design features.
This new one happens in Multiple Book Display (MBD) (latest Verbum; latest macOS).
Normally, to delete a highlight, you have 3 choices. You can re-highlight, for the highlight menu (optional), or the right-click menu.  Or just use the Notes tool.
But in MBD, re-highlighting to delete, is now ignored.  It thinks you want to just highlight and highlight some more. 
The recommended workaround is to simply keep 6 or 7 additional panels open, matching the MBD, just in case a highlight needs removal.  Being a bit ascerbic.