I found a bug - highlights aren't always being attributed to the correct chapter. It seems to have to do with the viewer thinking that as soon as the next chapter's title is within view that you are in that chapter. I assume this only applies to Flow Mode, and even then only applies to certain books (as most books seem to only flow until the end of a chapter, whereas this one doesn't do that - I assume there is something off with the chapter tags, but don't know how to (or even want to) fix this for every book that might have this problem.
Here are highlights when the next chapter is not in view.
And when you scroll down so that it is in view (note Chpater 12 being bolded in the TOC).
Even stranger: when I add a new highlight above the previous ones, it registers in chapter 12 because the viewer thinks I'm in that chapter now.