The one flaw everyone pointed out was keeping Wells’ ending where the aliens are done in by germs...at a time when the Germ Theory of Disease was fairly new this was novel but now it’s a cliche. But I loved it for the great action scenes (that rushing train!) and the entirely unexpected melancholy tone and subtext of how groups of people respond to a calamity. There are logical flaws in Hamlet and Macbeth too. No one cares.
I’ve seen many a flaw listed for the movie and nobody has mention that. The REAL major flaw is the idiocy of having the aliens come from beneath the earth, the whole idea that anything could hide under the soil in America is painfully stupid, laughably ridiculous, and turns the whole movie into a comedy.