Plot hole: The Voyager was continuously attacked by small Kazon attack ships. Yet the Captain never orders to increase the warp speed to evade them (In previous episodes we saw that the Voyager has much higher max speed than any ship in Kazon arsenal). They simply travel at a lousy Warp 2 and wait to be attacked. It would make sense to travel slowly if they were trying to avoid being detected by Kazon but that was not the case. They were attacked constantly. Voayger may be more maneuverable at slower speeds but if you can outrun your pursuers there is no need to maneuver to avoid them. Also, if Voyager was traveling at a higher Warp Speed, there would be no way for the Kazon to array fighter craft ahead of Voyager as they would not be able to overtake Voyager. If they could, there would be no reason to deploy the fighter ships, they could simply engage with their capitol ships.
Plot hole: Voyager has been traveling home for months on a long trip home presumably at high warp most of the time. However in this episode every kazon first maje is able to catch up to them in a short time frame.
Other mistake: At the beginning of the episode, as B'Elanna is working her way out through the doors, the Doctor cowers and tries to hide behind things. There is no reason for him to be afraid. He can't be hurt under normal conditions - this proves to be the case later when he feels pain and says he is not programmed to feel pain, and we learned earlier in "Phage" that he can change whether or not things pass through him.
Plot hole: In this episode Kes states that she has to decide now whether to have a child or not because Ocampa women can only get pregnant once and deliver one child. If that was the case they would have died out a long time ago, or never even evolved, as two people only getting one offspring would reduce the population to 50% of the original figure each generation.
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.
Continuity mistake: Dreadnought states there are fifteen priority targets approaching. On radar sixteen Rakosan ships are displayed. Then just before the Dreadnought attacks (and destroys three of) the approaching ships, there are a total of nineteen Rakosan ships displayed on radar.
Character mistake: As Voyager is bombarded by the cyclone, Paris reports that Voyager is at 20,000 meters and falling. 28 seconds later, he reports that Voyager is at 18,000 meters and states that, at this rate, they will crash in 10 minutes. However, if they drop 2000 meters in 28 seconds, they would actually crash in 252 seconds (just over 4 minutes). One might argue that perhaps it was calculated that their descent would slow down as they approached the surface, but later they fall from 2000 meters to 1000 meters in 14 seconds - the same rate.