OK, I can see the problem with these books. They all have a lot of images. And I think that is at least partly it. Some of the chapters page correctly for both the chapter and book, but, others get more out of sync with the number of images. I don't have many books with images in them, so that probably explains why I haven't seen this. And, it might be an issue introduced with image scaling added in firmware 4.21.15015.
I realised that one of the books was
https://www.kobo.com/au/en/ebook/what-if-56. So, I got the preview. The problem is visible in that. So, it is a problem with purchased kepubs as well as sideloaded.