When Ensign Kim is telling where to find the phaser drills he says "you'll find them in cargo bay 3." In season 3's "Macrocosm" Captain Janeway told the Doctor that he has access to the mess hall and "both cargo bays." Therefore the statement of finding phaser drills in cargo bay 3 is incorrect. Voyager only has 2 cargo bays.
When Neelix goes to the Holodeck to apprise Naomi of the latest developments, Naomi's arms change between shots (hands in her lap in one shot, arms crossed in the next).
The number of Naomi Wildman's cranial ridges has changed. She now has four, when previously she had three. Since they are most likely made of bone-like material, it is highly unlikely that their number would change so suddenly. At least this would be true for humans; however, Naomi is part-alien and the number of ridges might well change as the child ages. Compare with human teeth: children have a total of 24 milk teeth, whereas adults have a total of 32 teeth.
When the Delta Flyer was just about out of time to be rescued by Voyager the computer said that the oxygen would be depleted in 2 minutes. Even if they couldn't get to the Delta Flyer in time the away team could've gotten into environmental suits to escape that particular danger in the cockpit of the Flyer.
Naomi Wildman appears to be about six or seven years old, and Seven of Nine mentions a time when she was six, to which Neelix replies "...about Naomi's age...". Naomi can be no more than four years old at this point. She was born towards the end of the second season, and it has been stated frequently that Voyager has only been in the Delta Quadrant for four years at this point.
When the rescue team from Voyager searches for the missing crew members deep underground, aided only by a few flashlights, there is an incredible amount of light in the caves with no obvious source.
In the teaser, the boom mic appears as Naomi explains to Trevis what it's like to be an explorer.
Tuvok tells Samantha that his youngest daughter has been without a father for four years. This doesn't jive with the age of Naomi who is stated to be just younger than Seven was when she was assimilated which would make her around 5 years old. On top of that, prior to being on Voyager, Tuvok was travelling with the Marquis for some time before the caretaker incident meaning that his daughter would have been without a father for more than four years.