- An announcement that plays in the Spaceflight Terminal states that "over 5,000 people currently live and work" on Sevastopol. However, The Art of Alien: Isolation states that the station has a maximum capacity of around 3,000 inhabitants, with only 500 on board at the time the game's events begin.
- The Pilot's chamber aboard the derelict ship on LV-426 is far larger than it was in Alien.
- The melted hole that Kane used to access the derelict's cargo hold is located behind the Pilot's chair in the game. In the film, it was located to the chair's left.
- The Eggs in the derelict's cargo hold are grouped into depressed sections with raised ridges in between. In the film, only one of these sections was covered in blue mist, but in the game, multiple sections feature this mist.
- Despite the fact the Anesidora crew apparently explore the exact same area of the cargo hold as Kane, there is no sign of the open Egg that should remain from when he was attacked.
- Sinclair, the chief of the Seegson Security team aboard Sevastopol, signs his final archive log with the name Jake, yet his ID tag, found nearby, gives his first initial as "F".
- Parker's character model lacks the beard he had in the film.
- Dallas' jacket lacks the laces on the sleeves that can be seen in the film, looking more like Parker's jacket.
- Lambert's corpse is in a different position to that of the original movie.
- Jones is completely absent from the DLC and Ripley does not collect him on the way out of the Nostromo.
- The Working Joes depicted in the comic have visible pupils in their eyes instead of LED lights. Their mouths are also shut instead of slightly open as in the game.
- Marshal Waits has close-cropped black hair in the comic, contrary to his appearance in the game, where his hair is longer and snowy white in color.