Plot hole: The manner in which the Microwave emitter is used to vaporize the city's water would not go as intended. Microwave emissions coming from a device located inside of a train that has a very metallic exterior will unavoidably be affected by the photoelectric effects resulting from any microwave beam that is focused at the water mains below the train from within it. A fork placed within a relatively low powered kitchen microwave would encounter a similar effect.

Batman Begins (2005)
1 plot hole
Directed by: Christopher Nolan
Starring: Liam Neeson, Michael Caine, Morgan Freeman, Gary Oldman, Christian Bale, Cillian Murphy, Katie Holmes, Ken Watanabe

Continuity mistake: When Batman drives over the cop car, using his batmobile for the first time, he knocks the light bar off. Camera cuts and now the light bar is back on the car. (01:29:05)
Bruce Wayne: I'm going to show the people of Gotham that the city doesn't belong to the criminals and the corrupt. People need dramatic examples to shake them out of apathy. I can't do this as Bruce Wayne. A man is just flesh and blood and can be ignored or destroyed. But as a symbol... As a symbol, I can be incorruptible, everlasting.
Trivia: The Batmobile holds about 10 gallons of gas, but only gets single digits in mileage.
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Answer: This is actually true to the comics, where a regular thug named Joe Chill was the killer of Mr. and Mrs. Wayne. There is no connection between this movie/series and Burton's "Batman"; they are separate takes on the same story, which is why things can be radically different. Burton chose to alter the storyline to give Batman an even greater reason to go after the Joker, that's his decision. Nolan chose otherwise in his presentation of the Batman legend, sticking to the original story.
Twotall