I'll have to do more research, but at first glance I don't see any criticism (yet?) on Wikipedia: https://en.wikipedia.org/wiki/Longitude_(book).
I'd like to see a breakdown of the facts vs. what Sobel wrote. I read the book because I'm a mechanical watch enthusiast, and I was not disappointed in any of the descriptions of the Harrison timepieces or what made them work. I plan to go see them next time I'm in London.
I still recommend the book, especially to watch enthusiasts.