Scrivener has some good tools for marking small portions of text with significant phrases. Both inline annotations and linked comments work well for this, especially when you consider the Find by Formatting can search for key phrases and isolate by colour (for inline annotations). What you describe is really what this feature is designed for. You have a line of prose identified as conflicting with the canon, so you create an inline annotation right there, stating that. I like to use a semi-standard code system. So for that I might type in “CONF//” and then add any commentary after that if necessary, even including Scrivener links to the items in question that are conflicting, right in the inline annotation. Since this whole thing will be stripped out when you compile (by default anyway), it’s a useful tool for you to mark and analyse your text in a safe way.
Now, the main disadvantage to this method is that it doesn’t have a “grouping” search like Keywords or Labels do. It does however have a step-search, via the Edit/Find/Find by Formatting... menu command. In that tool you can constrain the search by typing in some text. So there you would type in your code, “CONF//” or whatever, and only those inline annotations that match that code would be selected when you go through with the Next/Prev buttons. This tool, like standard search, also has a “headless” mode that is completely keyboard accessible. Once you load the search term into the panel, you can close it and use Ctrl-Opt-Cmd-G to jump to the next match, or Shift-Opt-Cmd-G for previous.
Some people prefer Inspector Comments instead, which are in general principle identical to inline annotations. The main difference is you cannot see the reason for the note in the editor, without clicking on it to view it in the right Inspector sidebar. On the other hand, they do allow you to highlight the problematic text in question. So those are mostly a matter of taste. I prefer to use a mix of them depending on what I’m doing. Comments for long rambling thoughts and inlines for short high priority problems since I can’t just avoid them and I can see them as quickly as I can skim-read the prose.
Anyway, I hope that gives you some ideas.