I know what you mean. I think the problem arises from the difficulty in integrating the need for interactive game playing and setpieces with the attempt to create a coherent narrative. In the case of DEAD SPACE, there's no logic in the appearance of the monsters, other than the developers' need to create some sort of threat for Isaac to combat. For me, many video games have the same structural incoherence that Hollywood blockbusters do in trying to shoehorn their setpieces and moments of spectacle into their narratives.
But then, some Japanese games are just barmy, with abrupt shifts in tone and content throughout their length (eg, the YAKUZA games) - in a very good way, of course