After Grant and Shannon identify Sheppard, they tell Nicholas that Sheppard is at one o'clock (meaning he would be in front of Nicholas and slightly to Nicholas' right). However, Sheppard is behind Nicholas' back and over his left shoulder (which is seven o'clock).
Mr. Phelps tells Admiral Sheppard that his retinas were burned due to radiation from an atomic blast. Radiation is not what burns retinas during an atomic blast; intense light does.
Mr. Phelps states that the supposed bodies of the U.S.S. Concord's crew might have residual radioactivity. Biological tissue does not become radioactive by being ionized by radiation.