Welcome to the forums FernadoKL!
I believe that this is not the case, and only applies when the creature enters the zone in the first place.
And since it ignores flyers it does not.
Now it would make some sense if it did, also, when a flying creature started to guard in a zone with caltropes, you would think that it would take some damage from them, But I believe this is not the case, as the creature has already entered the zone.
Makes you think....