When Susan goes into the abandoned subway office looking for Manny, she calls out "Chuy?" and not "Manny?" Chuy is hiding in the office, but at that point in the film she doesn't know it yet; she has no reason to expect to encounter Chuy and no reason to call his name. In fact, as far as we know, she shouldn't even know his name.
Near the end when Dr. Peter Mann is running from the female Mimics, he does end up in the larva room and gets the idea using his lighter and the gas to neutralize the upcoming threat with fire. When his Lighter does not function anymore and he loses it in the water he gets the idea to use sparks created by the pickaxe, which worked quite easily. However whilst all the gas pipes where metal and you hear the sound of metal hitting metal, there happened to be no single spark while he hit a dozen holes in them.
In the last scene where the male bug is struck by the train, you see it struggling to hold onto the front of the train for a while. It manages to hang in there for a little while before being pulled under and splattered everywhere. But when Dr Susan looks around the corner, after the bug is killed, she sees parts of the bug just meters away from where she was hiding. The bug should be further down the tracks, because it was dragged for ages before going under.
After Leonard and Dr. Mann fall, Dr. Mann instructs Josh to thrown down the glow sticks. He's still writing the instructions on his hand when he leaves, he never throws down anything. Neither of the 3 characters do anything that would indicate that he does. Later you see Dr. Mann using glow sticks that shouldn't be there.