This is one of those topics that gets brought up and hashed over time and time again. Basically, no word processor, text editor, or word manipulation tool is ever going to get it right because the software has no idea what is and isn’t unique words. Scrivener, like pretty much all such tools, counts every addition and subtraction regardless of where it came from - it has no idea if what you are doing furthers the story or whatever, it has no context to it. You are the only one that can put meaning to the relationship of your adds/subtracts/edits.
Asked and answered multiple times - Scrivener provides various ways to make it work how you would like to see it (with some issues that just are not possible to fix). You can read through these forum threads:
[url]Windows 2.9.9.9 HiDPI - Spelling Check Squiggly Hard to See]
and, [url]How can spellcheck's red dots be made bolder?]