I've noticed a few control anomalies as well, which is a problem since I tend to remap controls pretty extensively.
For example, if I leave activate as the default "E", it works as advertised. But when I remap it to my mouse's first thumb-button, it works fine for activate, BUT if I activate a book to read it, it won't work to take the book, nor will E (or any other key - believe me, I've tried 'em all!).
So basically, when I want to take a book, I'd have to remap Activate back to E, hit E to read, then hit E to take.
For now, I've just stuck with leaving activate set to E, which is a mega pain in the butt since I'm so used to clicking that mouse button in every other game.
I also can't seem to get Favorites working (and btw, why is there no "u" in that? I live in Ireland, we use UK english, which spells it favourite... poor localisation, perhaps?)
Maybe if I reset everything back to default, it might work. Next time I come across a book, I'll try that and report back.
Another annoyance - I always remap quicksave/load to f11/f12, but I cant do that here - f12 is 'reserved' for some reason, but I can't see what for - it doesn't seem to do anything when I hit it in game.
I've had a root around to find an INI with the control mappings to see if I can resolve it with a bit of judicious text-editing, but I'll be buggered if I can find the controls. Maybe stored in the save file?
Having said that, I'm about 2 hours into the game, and I'm really enjoying it. It looks gorgeous, and I reckon I'm going to sink a few years into it, between playing and modding. Happy days!
