The first deleted scene is of Mark (Paragon) gaining his powers. This was originally included in the first chapter, but was removed from the first version of the script because I just wasn't comfortable with writing what starts off as such a real world event that regularly costs lives. The later Afghanistan scenes were awkward for the same reason, but were more embedded in the story, and the action there was more fantastical.
Deleted Scene 1
The second deleted scene, which has been in and out a couple of times, is to show the Project members using their powers in assisting with a non-combat emergency. It was only removed because it wasn't adding much to the story, and I'm still not certain that was the right decision. It would take place between what are now chapters 7 and 8.
Deleted Scene 2