The majority of them were due to the fact that they set up these aliens to be far too invincible early on. You can fire a hundred rounds into the alien and it won't go down, and there are drones all over the air that can spot any movement on the ground and destroy it with heavy firepower. So as a result:

- the idea to board the bus was suicidal. They were taking out all this movement, literally the entire area is abandoned... and you want to roll out in a huge fucking bus?

- Eckhart's Hurt Locker moment where he goes it alone to take out the drone, and the ensuing "that was some John Wayne shit... but we wouldn't have survived without you" moment after.

- the aforementioned Michael Pena grabbing the gun and killing the alien, the same type of alien that a Marine shot a hundred times and couldn't take down, proving that his character ONLY existed so that we could watch a cute kid cry for his zero-dimensional daddy.

- the revelation: "where would you keep a command center?" "... UNDERGROUND!"

- the pulling the command center out of the ground (how it got there is anybody's guess) to "fix it"-- why was that again? I don't recall it being satisfactorily explained, and if it was explained, the point was moot, since the REAL reason they pulled it up out of the ground was (a) to show off the movie's only cool special effect, and (b) to make for an easier target for the humans, who would have had zero chance to win had the aliens had a way to fix it while it was still underground. The drones were still flying after the command center was hit... soooooo why not just leave the rest under there?

Then again, I'm wasting time trying to apply logic to a film that didn't bother to ask questions of logic in the first place. All I want is a sci-fi alien movie with good characters and good suspense. Several have been made already. But if you can't give me at *worst* a fun time at the theater, and instead you want to make it very glum and serious, why not flesh the characters out and ask the questions about logic in the making of the film?

*walks away from post*