While checking his/her scavenger disguise in the mirror, the reflection of Munro's weapon position doesn't match the first-person position.
According to Voyager's library, Zefram Cochrane's first warp flight and first contact with the Vulcan occurred in 2061. However, the date for both events was given as April 5, 2063 in Star Trek: First Contact (1996).
In the Virtual Voyager subgame, Harry Kim's quarters are on Deck 2. However, they were established as being on Deck 6 in Waking Moments (1998).
The inside of the scavenger base does not match the outside.
Backwards writing can be seen on some panels.
The windows on the U.S.S. Voyager - such as the windows by the Mess Hall - do not match the windows on the outside.
The Shuttlebay is on Deck 10. It is supposed to be several decks lower.
The door on the fore end of the Shuttlebay is not big enough to allow for the ship's other shuttles to make it through from the storage bay.
The part of the scavenger base that was made from a Federation starship was said to have been made from a starship of the early 23rd Century, but it is a mid-century ship.
In the locker room prior to the dreadnought mission, Biessman says that he thinks that Murphy was a Bolian, referring to Murphy's Law. Chell asks who Murphy is. However, one of their team is named Telsia Murphy; in all likelihood, Chell would have assumed they were talking about her.
Although the Virtual Voyager subgame is intended to take place prior to the Hazard Team's mission to the Forge, the ship's library refers to the space station's destruction as if it has already happened.
The aliens aboard the spaceship never ask for their weapon back if the Player takes it.
Dilithium crystals are relatively rare in Star Trek canon, so their use as weapon consumables makes little sense.