I love puzzles, but the two you mentioned did kinda put a crimp in my enjoyment. I actually utterly broke the Immaculate area, because my first time there I just picked the lock to the side room, strolled up to the blood stone, and then figured I had finished up there accidentally. I didn't even notice that I could go *down* from there to actually move the story along.
So, upon my return from the Homestead, I thought, "Crap, I bet I needed to actually go through the quest." First door I touch gives me the Rot, which can only be cured via a Blood Stone... which I had already used up an hour ago. Then I got stumped on the pressure plates, because I couldn't find the proper items to get them weighed down. 2/4 worked, but I got frustrated with the last ones. I wound up working backwards and picking locks all over again, which further broke the quest line.
And when I finally *did* get back to the proper place in the storyline, the guy accuses me of cheating because he claimed I didn't have the rot. Which I did. -_-
As for the buttons? No damn idea how I solved it. I randomly mashed until the door opened and I got the blood. There should definitely be some kind of extra hint or somethin'. I mean, the huge compass on the floor felt like it should've been a hint about how to do the buttons, but I never found the reasoning for it.
So yeah. Some puzzles and game logic wind up crossing wires in the game, but most of the challenges are pretty darn good. Overall, I still adore the game.