Just resolved one of ending plot holes. Never heard this bit whilst playing the game, but it does clear things up.
Was watching a youtube clip of the part where Shepard, his/her squad and the rest of Hsmmer are rushing towards the Citadel Beam. After Harbinger slaughters them all (minus Shepard and Anderson), you see Harbinger leave and the Sword Fleet commanders panicking as no-one made it to the beam to activate the Conduit. With the mission seemingly failed, the Commanders order a retreat, telling ships head for the relays. This explains why the Normandy was in the middle of a relay jump when the Crucible went off, although not why Liara, who was with me why i was going for the Citadel beam, appear unscathed after the Normandy crashed.