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: 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.