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.
Continuity mistake: Tuvok and Paris' rank seems to skip around during the first season. Despite being listed in the credits as 'Lieutenant Tuvok', Tuvok starts the show as a Lieutenant Commander, with the signatory three collar pips, one black and two gold. At certain points, however, he is seen with only two gold pips (signifying Senior Grade Lieutenant). After season one he remains a Lt. Commander with no reason for the lack of continuity offered. Similarly, Paris starts the show as a Senior Grade Lieutenant, but sometimes instead of two gold pips he has one gold and one black, the signifier of a Junior Grade Lieutenant. After season one he is always presented as a Junior Grade, excluding his brief demotion to the rank of Ensign in a later series.
Factual error: To protect the warp core, Janeway instructs Paris to move away from the rings at Warp 7. Moments later (Janeway, Torres and Tuvok are still in the same position), Paris tells Janeway they are 0.6 light years away from the rings. Warp 7 is 656 times the speed of light. It would take about 8 hours to travel 0.6 light years at Warp 7.
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.
Character mistake: When trying to trap the energy mass they created, B'Elanna announces, "Now it's trapped on three sides," to which Paris replies, "It's changing course. Heading for the open side." Since we function in 3-dimensional space, unless they are trying to trap it in a triangular-based pyramid, the number of "sides" to be concerned with is six.