You have an alien that needs his special blocks to make his spaceship and you ship both the alien and the blocks in the same friggin' train?? I would have them at other ends of the damn country!!
And why were they moving the alien in the first place?? Was that ever explained??
For a change alien wasn't the bad guy. I always thought that if we ever encounter alien life more advanced than us, it will be us who will start a conflict. For various reasons. Major one being, lack of understanding. Mainly because we're so high up our a*ses we would still think that we're on top of the food chain. And if military did what they did in this movie. represent humanity in a hostile manner... too bad for us all.
The increase in human knowledge is the cause of the decline of religions.
Being of higher intelligence also means the alien was an apex predator. In nature the predator should be able to be smarter than its prey in order to hunt it down.