Plot hole: To escape the 'event horizon', a rupture in it is widened to 120 meters (which allows 2 meters clearance on each side of the ship). Soon after, the rupture has shrunk to 110 meters wide, and Janeway decides to 'punch through' anyway. The ship does so with little difficulty, but the whole issue seems pointless since the rupture was far larger 'vertically' than 'horizontally' (relative to the view from the ship), so tipping the ship on its side would have allowed plenty of clearance to slip right through.
Plot hole: In the beginning, when the doctor is activated, he immediately asks who activated him. The computer tells him he was activated when a red alert was initiated. But then he finds out no one is on board, so there was no one to initiate the red alert at that moment. He should have been activated much earlier, when the crew was still on board and under red alert, even in a simulation.