5) How does 1 photon torpedo Destroy General Chang's BoP in ST6, but 72 photon torpedoes blowing up INSIDE the Vengeance only "disable its weapons systems"? That thing should have blown to Kingdom Come. I don't really know an elegant way to have fixed this in the script so that the Vengeance could still be piloted to collision course with the surface... Maybe Bones was only able to arm 3-4 of the Warheads in time? Even so, an ordinance explosion of that magnitude within the hull still takes most ships down.
The novel stated that they only armed one torpedo and that Khan had scanned a few but not all of them. So Spock was playing odds that the one torpedo armed would not get scanned. (I might need to re-read the chapter for more specifics).