a) This has annoyed me for quite some time:
With page numbers turned on when the highlight is applied:

With page numbers turned off when the highlight is applied:

logosres:mishnah;ref=Mishnah.Pirqe_Abot_4:17_B
I don't want the page number highlighted. It's not part of the text. Plus it makes it black and therefore much more visible. And I don't want to have to turn them off and then on again every time one happens to turn up in the middle of something I want to highlight.
b) In this particular case I also don't want the 'B' highlighted, but I don't expect there is much you can do about that? Though it is rather annoying in a resource like the Mishnah...
c) Sometimes the page number gets highlighted by itself later, even though it wasn't from the start. In the case above, all I have to do is to right-arrow through my three parallel resources, and when I come back, the page number is highlighted in spite of all my efforts.
d) Even if I start with the quotation mark -- avoiding both the 'B' and the page number -- the page number still gets highlighted. Regardless of whether page numbers are on or off when I apply it.
e) A keyboard shortcut for toggling page numbers on/off would be welcome.