I think maybe what you're hearing is a very quiet 'gulp' as the G4 note takes over from the C4. As Herb says, it's a natural sound made by the instrument's keys. To me it sounds like part of an organic flute performance (which of course is what it actually is, as the legato intervals are all taken from real life note transitions.)
It's possible we're not hearing the same thing (and I agree that's it's difficult to accurately describe the subtleties of sound in words), but to my ears this little noise helps the legato interval to sound real - if it wasn't there, you'd hear a straight C4 sample followed by a straight G4 sample with nothing in between to help join them together in real legato style.
Flute 1's 'sus vib' samples don't make this sound, so you could use them instead if it bothers you.
The other thing to bear in mind is that when you close-mic an isolated instrument you hear a lot of detail you wouldn't normally notice, such as squeaks, buzzes, key clicks and so on. When you add reverb or other instruments these sounds become less noticeable, but they probably still play a subliminal part in achieving an overall realism.
