I think people look to deep into this movie. Aliens work in mysterious ways. We aren't supposed to understand these things. The Indy movies have a reference of what some people have spent their whole lives searching for (the ark, the grail, UFO's) The thing is that the first three films had years of history, and many books to back up evidence and all that crap. Where as the 4th Indy film is based on very little knowledge about such a thing, and one person's take on it. In this case lucas'. No one knows what alien can or cannot do. It's a matter of what we think they can do.

Lucas brought up some really clever ideas and turned it into a movie.

-Mayan hieroglyphics that look like flying airplanes
-The landscape pictures in peru that can only be seen from the sky
-Legend of the crystal skulls
-UFO crash in Roswell
-The fact that ancient civs were highly advanced

It's very clever in my opinion