The ...world_sites... file correctly showed the site as belonging to the dorfs. I've zipped it up in
https://www.dropbox.com/s/swtois5351dmh67/Dwarf%20Fortress%200.44.12.zip?dl=0.
This zip file contains two sets of exported info. The earlier one is the one containing the issues mentioned, while the later shows is a "bonus" issue: The Necro tower Machinesprings (just south of the mountain block in the northern end of the map) throws an exception when clicked on (and doesn't show any info when hovered over). I suspect the tower to be completely empty, as I've raided it repeatedly and had a couple of raids report it just being searched, while most reported reported the dorfs slipping in undetected. Since you can ignore the reception and return from it it's not a serious issue, but it does block you from seeing the info on that site (like the slab the dorfs failed to bring back).
Back to the original issues: The books stolen were taken from the same necro tower mentioned above, i.e. Machinesprings. "The Secret of Creation" is listed as (created, stored) in Machinesprings, and listed as stored in "Newhope the Future of Knowledge", my fortress, to the south of Machinesprings. I suspect the logic looks at "stored" in the log for the book, but fails to account for the next entry "stolen" (i.e. no longer stored), when looking at the info on the book.
And the first issue: There's a civ connection line from Newhope to the SE to Seizerained. Two tiles to the west of that site you have Birdtufts, which is shown with goblin civ links, but it was in fact conquered by me (and the detailed info shows that to be the case, which is probably what you extract from the ...world_sites... file). The issue is that the civ level lines don't match that (and the screen on the doesn't list the sites. However, the summary screen lists The Sin of Clobbering as having 2 sites, while the world map shows 3 (the third one being the misrepresented one).
I hope I've managed to explain the issues. If not, please request clarifications.