The arrangement of the wagons. Ok, they didn't show every single one but kindergarden after slaughterhouse and the club full of druggies next to the engine? The Terminator/Superman guy. Apart from beeing immortal, he just goes ham on his own people for no reason. Then the stopping the engine with his arm. Yes, it fits the story but come on. There's a table right next to you....and of course the ending. The in your face happily ever after just doesn't work with all that happend before. A more subtle like blending off when the girl/boy awake after the crash would still project hope, but without all that sugar coating.
Also didn't understand the fuzz about the bugs protein bars. That's some damn good protein and as long as it doesn't resemble the animal, I see no problem.