Dead Space takes place on board the the USG Ishimura, a colossal "Planet Cracker"-class mining ship. It's a ship designed to literally rip apart planets to feast on the tasty, tasty ore inside. The ship's architecture varies from tight constricted maintenance corridors to huge open industrial spaces. At various points you visit the hydroponics bay, personal quarters, the medical bay, the bridge, and pretty much the entire set of possible important ship locations.
Most of the places you travel make sense in context of the ship's purpose. There's equipment suitable for its purpose, the layout is at least plausible, the lighting looks like it would be acceptable before zombies smashed up the place, etc. Some of the places do not make such sense. The ship is weirdly infested with inexplicable circuitous corridors. There are industrial areas that can best be described as mazes of walls. Why is there a maze in this ship? Did the crewmen just want a maze in their ship? There are strangely-placed high-speed trams that lead from one near-dead-end to another (the asteroid cannon being the most notable WTF moment). Why isn't, you know, there just a door which is closer? Are you seriously saying there aren't any other corridors within a kilometer? Overall, a good chunk of the ship just plain doesn't make sense.
Now, if the ship were designed by zombies – yeah, sure, go for it, zombies are crazy, who knows how they'd design it. But they aren't. It was designed by people. And when you're told that you're walking throughout a human-designed spaceship, and 3/4 of the ship makes perfect logical sense, those moments when you find yourself thinking "wait, why does this area even exist?" are painfully jarring. Why does this maze exist? Well, it exists because the game plans called for a maze, and by gum, we're putting a maze in!
What's the fix?
The only fix I can think of is to be excruciatingly careful that each location makes perfect sense, both for the game and in the context of the universe. It's hard, it's really hard, but I think it's important. This isn't an issue that's restricted to games – it's something movies get constantly wrong as well (please, explain to me why the Emperor's chamber on board the Death Star has a hole leading directly to the reactor core without even a guard rail) – but that's not an excuse, it just means we get more people to laugh at when we finally get good enough to avoid it.
For each zone, for each object in the game, you have to answer two questions. Why does the game contain this? Why does the world contain this?
If you can't come up with good answers to both questions, get rid of it.