In chapter 12:
-"She wouldn't? But why not?" Athrun groaned, exasperated.
Meer talking, Athrun responding, on the same line. Again, confusing.
-"Of course." The officer she had addressed as Heine replied, then turned to Athrun. "There was so much going on yesterday that you and I were never properly introduced. I'm Heine Westenfluss, of the Special Forces. It's a pleasure to meet you, Athrun."
Do you want Heine to be this casual, here, using Athrun's first name already? And it seems funny that Athrun sticks to calling him "sir" regardless.
"Hey...that's the girl from yesterday." He mumbled, the memory of the incident still causing him to blush slightly. He smiled, closing his eyes and listening. Then he heard a sudden cry, quickly cut off, and a splash.
"Hey...did she fall over?" He asked, slightly nervous. He ran over to where he'd last seen her, and sure enough she had fallen in.
Having Shinn talking out loud to himself doesn't make him appear the sharpest tool in the shed.
Use inner monologue for reflective thinking, you can either write that in (e.g. Shinn recognized her as the girls from the day before, and the memory of the incident still...) or use cursive to show an inner monologue (which seems to be quite standard).
-"It's...kind of a long story." Shinn said vaguely. Athrun rolled his eyes, and he piloted the launch - a big RHIB* - close enough for Shinn and the girl to get in. Then he turned around and headed back towards shore.
What's a RHIB? I thought the asterisk promised an explanation later on but I couldn't find it...
In the Jeep, Shinn turned to look back in the direction the other car had gone, hoping that, as unlikely as it seemed to him, he would see her again...
Now that you mentioned it, I suddenly had to wonder that even in GSD they never got so far as to change cell phone numbers. I would assume those still exist. Of course, it isn't important for the plot as such, but just a small tech-gap I noticed. No changes required.