In Chapter 1, the faces of the other marker test subjects on the computer in the observation room, are actually members of the UI Development team.
Contributed by ProtoSnake
In Chapter 1 in the area with the first shop, there is a working scale that shows Isaac's weight at 195 pounds. After he equips his Engineering Suit, he weighs 255 pounds.
Contributed by ThisGuyInTheSuit
In Chapter 5, if Isaac lets Spoiler: the Tormenter kill him in space, a hand will float through space, as an homage to the original Dead Space cover.
Contributed by ThisGuyInTheSuit
There was originally going to be a necromorph called the "Flytrap", but the enemy was scrapped sometime during development. It was going to be both an environmental hazard and a regular enemy, intended to encourage the player to slow down, without feeling like an artificial gameplay mechanic. Both of its hands and feet would be stuck to a ceiling, and the skin on its stomach and chest is missing. It would have used its internal organs as a dangling lure, and attacked the player when they got close.
Contributed by frankfrost2