Quite simply, in all likelihood the pilot looks at his clipboard, it says "1 passenger from X to Y." He goes to X, picks up 1 passenger, goes to Y, drops off passenger, checks next item on clipboard. End of story.

I wouldn't be surprised if Nathan told the pilots flying back not to ask questions who comes along.

• a pilot might wonder how a woman could get to this deserted areas if she was not a guest at Nathan.

Of course, any number of things that could've played out. Is it also possible that she'd taken a look at the
https://www.google.com/search?q=list+of+helicopter+controls
and stuffed the pilot into the back.

Pilot: "Hey, I was supposed to pick up some schmuck, not a pretty little thang like yourself"
Ava: "Oh, you mean Caleb? Nathan wanted him to stay for another week to work on new developments. They sent me to back to HQ instead".
Pilot: "Makes perfect sense. Strap in!"
Plothole plastered and sealed forever.

An unanswered question isn't a plot hole.
We try but we didn't have long
We try but we don't belong
-Hot Chip (Boy from School)

I just finished watching it and wondered that myself. Maybe the security is so tight that the helicopter pilot wasn't told who he'd be collecting? I dunno. Great film though!