Huge plot holes

Maybe I'm slow on understanding the movie, but there were a lot of things that seemed totally illogical. I know it's a fantasy movie, but even in a fantasy movie the story should make sense.

I could have missed the explanations, but these are a few questions that bother me:

How can a small pickup truck totally destroy a mile-long train simply by running into it?

And why is the pickup truck less damaged than the train?

Why did the alien wait for the crash to punch his way out of the boxcar, if he could have done that any time he wanted?

Also why did the military put him in such a flimsy containment in the first place?

The alien is much more intelligent than the humans, and just wants to rebuild its space ship so that it can go home, so why didn't it rebuild its space ship when the train crashed and it got out of the boxcar? (After all it had not only the cubes that made up its ship but also tons of metal from the train itself and the tracks, and it had plenty of time to do it before the military arrived.)

Why did the alien go to the time and trouble to open the hoods on all of the cars on the used car lots, carefully take out the engines, and close the hoods again without leaving any marks, when he could have more easily just taken the entire cars and had all of that extra metal?

The alien killed the military men that were attacking him, but why did he waste time going out of his way to abduct innocent people like the girl, and why did he hang them upside down in his cave?

Why did the alien build his ship and take off in it right after listening to the boy, when his goal was to do this all along, and he could have done this before he chased the boy and the others?

These are parts of the plot that make no sense to me, and spoil what could have been a much better movie. Maybe I just don't get it, but I'd really like to find out if there are reasons that I may have missed for these things, or if they are plot holes that other people are also trying to make sense of.