The Problem: Ok, technically this probably isn't a bug, but it's a significant UI useability issue 
If you use Logos for any length of time you end up with lots of Notes documents. I have over 40 and I don't even use notes that much, I just like to create a new note file for each thing I work on to keep a few relevant notes together. The problem is all the bibles automatically default to having all the note filters turned on if a note file has a bible reference in it, so if you're reading a passage and you want to turn off the mark-up and it's not clear which note file is the culprit, you have to go through them one by on...
My suggestion: have a check box at the top to turn off all the notes and highlighting, here's a mockup of what I mean:
