5. Why was Batman unaffected by the toxin when he turned it on Crane? He was right next to him.
Because he'd already been inoculated. It's the same reason why he, Rachel, and Gordon were unaffected when the fighting in the Narrows occurred.
Honestly, ender, I think your list is much nit-pickier than a lot of the problems people have been talking about with this movie. Not to mention that, and I can't speak for everyone, but most of the my own problems didn't seriously affect my enjoyment. Some were more damning than others. Others were just slightly silly.
I do find it odd, though, that in that whole big list of yours, you didn't mention the one glaring problem I had with BB: the whole first scene where Bruce declares his intentions not to kill. He tells the League of Shadows to stuff it. He will not kill people. Then he blows the whole place up, most likely killing everybody except for Ducard. That prisoner didn't seem in any shape to escape the blast. I mean, he was tied up, so he probably died anyway. So instead of killing one man because it's morally wrong, he ends up killing everybody except one man, and it's not even the man he was trying to stop from killing!
In your scene where you're trying to express the thematic importance of not killing people, it really hurts to punctuate that point with a big explosion showing bodies flailing through the air. At least with the Batmobile and train sequences, while it's implausible no one was killed, it's not impossible. In this sequence, it's like they went out of their way to show as many people die as possible.