as I said, I think he was more concerned with the "big picture" of the themes he was trying to address in the movie and so he didn't really care about those other details.

>suppose for a second they're highly advanced Borg-like
>conquerors... why would they be messing around leaving
>geometric signs in crop circles? ... exactly

nope. there is at least some sense of mystery to that, like you are trying to figure out what the hidden meaning is behind it. hence suspension of disbelief can work there. the water killing them/can't open a door stuff is just plain fucking retarded.