The location of the train crash. Why the teacher would do it right outside of his town as opposed to anywhere else in the country. Was it possible to do it somewhere with less people? The teacher apparently didn't care about the risk to the people to do what he did.
I don't think it was wise to try and make a creature that eats town folk sympathetic, even if he did suffer at the hands of the military and just wanted to go home.
The water tower thing wasn't clear, and not sure why it was necessary exactly. (though I think he created a machine to bring all the cubes together with a magnetic field) I question why the magnetic field pulled away some metal stuff, but not others (some guys guns, but not all, etc.). I question what the deal with the locket was. Sure it's a nice touch for the kid to symbolize letting his mother go, but what did it have to do with the machine? It sure seemed like it was the last piece to get everything to come together for whatever reason.
The connections with the monster...surely the monster could have figured out from any of the others that they all weren't out to harm him and they all have difficulties too (we know for sure the girl has problems going on in s similar vain to the Joe). So, why only when he connected with Joe did he stop and go home. And why is he still out collecting people if he's got everything he needs to go home (assuming the stuff under the tower is what he needed for that).
Also, this point (which I borrowed this text from someone's review since I'm lazy):
Because the kids have no effect on the story, not the military’s interference in the accident clean up, not the finale, etc., etc. If you took the kids out of the movie, the outcome would be exactly the same. The Super 8 reel that they are so excited to see makes no difference with regards to their behavior either, so it’s almost as if the entire movie is a MacGuffin.