During the climax of Dark Skies, the aliens came down to the house to take their subject. The house was boarded up so the aliens couldn't get in and you could see very bright light coming from outside, an obvious alien intrusion. So how come none of the neighbors, who already knew something weird was happening with the family, didn't see anything? Furthermore, why did no one hear the shotgun blast?
The aliens could appear and disappear at will, enter the home without coming through any opening, open every door simultaneously, and control their sons mind to lure him out of the bedroom where they were making their last stand. So showing visuals and sounds that only the occupants of the house could see and hear has been established throughout the film.
I think the real question/flaw is with them all huddled in the master bedroom at the end why would they let the son wander over to the door, open it, and casually stroll straight to the aliens?
In retro-spec, my second paragraph is answered by my first, ironic. Any application of normal logic to this film given the writers carte blanche of "anything goes" is the actual flaw.
It's hard to say because there weren't any neighbours to be seen in the scenes after the abduction scene. The first scene after it shows an article in the newspaper about the parents being suspected from making their son disppear, but that's all we get. It is possible that neighbours heard the shotgun blast, though, but that wouldn't indicate aliens being involved. Not for them.
I think the writers didn't put too much effort in covering this part, leaving it open to our imagination. It could be that the aliens somehow kept the neighbours in their sleep, after all they did have some supernatural powers. (And, they presented themselves as the 'Sandman' :p) Of course, this is just speculation.