When Janeway and Tuvok are going to check on Harry, they say to the computer in the turbolift, Deck 6. However, Harry in the episode Alter Ego said deck 3.
In the first conference room scene, Captain Janeway asks "Where's Harry?" Some people have stated that it sounds like "Where's Garrett?", i.e. Garrett Wang, but it IS "Harry" she mentions.
When Chakotay gives the Doctor the order to destroy the cavern with the aliens and their transmitter he says to give him 5 minutes. When he (Chakotay) falls asleep he tells the aliens that it'll be destroyed in less than 2 minutes. The elapsed time between when he gave the Doctor the order and telling the aliens is only less than a minute. So this statement is not correct.
As they are escaping engineering, for a few frames, Roxann Dawson's pregnant belly is clearly visible as they rush out the door.
While in the cavern, Chakotay chooses to inject one of the sleeping aliens rather than himself, but he could have easily injected himself and requested another injection to be beamed down by the doctor. Equally, Chakotay is prepared to sacrifice himself to kill all the aliens, but the doctor could just beam him out before the attack.
Borg do not sleep, they regenerate. Seven should not be in a rem sleep state.