Ayala refers to himself as Ensign, and Janeway responds in kind, however he has always been a lieutenant and there is no reason for him to have been demoted.
When Janeway drops the force field to go into the cell with Seven of Nine, the guard is ready, in case Seven tries anything. His phaser is briefly seen in his left hand, but when the camera angle changes, it is in his right hand.
Janeway tells Kes that she was with Tuvok when he got his meditation lamp from a Vulcan master, "Who doubled the price when he saw our Starfleet insignia." The Federation, and especially the Vulcans, do not use money.
This episode takes place in the year 2374, and Captain Janeway estimates that Seven of Nine's capture by the Borg happened "around 20 years ago", or 2354. But just four episodes later in "The Raven", this was changed to show her assimilation occurring at age six in 2350. The Season 5 episode "Dark Frontier" places her birth in 2344, which would make the character approximately 30 years old in "Scorpion Part II", her first appearance.
When Kes is destabilizing in the mess hall Tuvok states that her body was in a state of Cellular Flux for 17.4 seconds. However the scene only shows her being unstable for 10 seconds.
When Seven of Nine's more human form is revealed, the size and shape of her head have changed considerably without any in-story explanation. This is because her previous "head" was a latex cap over Jeri Ryan's voluminous hair.
When Seven of Nine attempts to communicate with the Borg Collective, the alert is not heard in Lieutenant Tuvok's quarters, despite Lieutenant Tuvok being the head of security.
Up until the moment when Seven fully realizes her isolation from the Collective, she generally refers to herself as "this drone" or "we/us," which is typical for a Collective-bound Borg; however, just after awakening at the beginning, she accidentally says, "*I* can't hear the others," and later, when revived in sickbay, "What have you done to *me*?"
When speaking to Seven of Nine, Janeway refers to Voyager as a "human collective" and a "human community." This ignores the numerous non-human crew members serving aboard. Federation ideals are more inclusive than that.