The Doctor tells Captain Janeway that there are seven people aboard Voyager other than her. However, there are only six: the Doctor himself, Tuvok, B'Elanna Torres, Seven of Nine, Neelix and Harry Kim.
The scenes at the end where the new astrometrics lab is discussed do not correspond to the same scenes at the beginning of part 1. In part 1, Harry and Seven of Nine unveiled the new lab to the command crew and explained that they could use it to chart a new, faster course to the Alpha Quadrant. Here, the command crew is gathered on the bridge when Seven of Nine announces that the new lab is online. Janeway then asks when they can plot a new course, without Harry and Seven explaining the capabilities of the astrometrics lab to do so, as in the original timeline.
This two-parter takes place over the course of a year, yet no one's hair grows the entire time.
After The Doctor relieved Captain Janeway of command, it was his duty to inform the other officers.
The Krenim time ship attacks numerous advanced, space-faring civilizations, yet none are ever seen to mount any sort of planetary defense.
Annorax immediately declares each temporal incursion a failure as soon as he is informed that the colony on Kyana Prime has not been restored. At no point does he consider that his family's history may have been altered and they may be alive and well on the Krenim home world or somewhere else.
Annorax says to Chakotay and Paris that, while Janeway told him their vessel was trying to reach home, he hadn't realized how far away home was. In that same conversation, which took place 2 months prior to the conversation with Chakotay and Paris, she had stated home was 65000 light years away.
When running into the burning Deflector Control Room, Janeway grabs a slab of metal to use as a shield. Metal conducts heat. The material she chose would make an incredibly poor shield against fire, and would actually actively harm her by holding onto it.
When informed that only one warp nacelle is functional, with the other being, as Torres puts it, "a lost cause," she orders all power to the remaining nacelle. Warp nacelles have to work in pairs to generate a warp field. One good nacelle won't do anything. Without both nacelles functioning, the ship would be limited to impulse power, and the impulse engines are separate from the warp nacelles. Diverting power to the nacelle would be a waste. That power would be put to better use diverting to the impulse engines, defenses, weapons, life support, or any other number of vital systems.
Tuvok tells Seven of Nine that it is inappropriate to openly contradict the captain in front of the crew. There is no remaining crew onboard, only the senior staff. The senior staff is allowed to openly discuss ideas, plans, and courses of action in a way that they would not do were there anyone else present. In the same conversation, he also tells Seven of Nine to remember the maxim that "the captain is always right." This is a highly illogical statement, as he is aware of Janeway's shortcomings as an emotional human being. He has often offered her counsel in the past.