Most disturbing scene in the movie was...*spoilers*
When the alien sucked up those people to digest them, and we got a glimpse of their "journey" through its innards/guts. That was fucked up and just claustrophobic as hell. Imagine being sucked up like that, knowing that you're being eaten alive and there's nothing you can do about it.
It actually reminded me of a scene in Dragon Ball Z. In one episode, Imperfect Cell opens up his tail into a large funnel (in order to swallow Android 17), and the camera briefly zooms inside Cell's slimy red tail. Link to the scene below.
https://www.youtube.com/watch?v=VdEpPLwsaww&t=7m55s
Here's that moment from Dragon Ball Z (Abridged was the closest thing I could find, but this moment is in the original as well).