Revealing mistake: While tossing a baseball with his son, Ray calls him a "dick." If you look at his hand at that point, one can notice that his hand is closed in a fist, and he is not holding the baseball he is prepared to throw. (00:10:10)
Revealing mistake: Dakota Fanning cannot actually see the computer generated birds that are flying high over the Hudson-Athens ferry. If you look closely her eyes stair straight ahead and not up in the air where they should be. (00:58:35)
Revealing mistake: When the Hudson Ferry captain casts off the large label that reads "Hudson Ferry" is on his left side of his jacket. However, in the exterior shot as he looks out the window at the whirlpool, the label is on his right side. This shot was flipped, and amusingly, the CGI guys actually retouched the words "Hudson Ferry" so it wouldn't read backwards. (01:02:25)
Revealing mistake: When the tripod is tipping the ferry over, people fall over the rail and cars slide toward it. You can see the cars stop short of the rail so they don't smash into stuntmen, even though they are jammed against the rail in the next shot.
Revealing mistake: At one point when Cruise is driving through the county in the van, you can see that the van is actually in "Park." You can notice this because the column mounted transmission lever is all the way up.
Revealing mistake: After the ferry scene, CGI clothes fall off from the sky, but manage to go through the branches of the trees, without becoming entangled in them, or without the branches affecting the falling path of the fabric.
Chosen answer: In the original George Pal version they were Martians and the reasoning for what they were doing was never explained. In this version, it's never explained where they come from, but their mission is simple, to eradicate human life from Earth, and use our bodies to fertilise the planet, probably so that they can colonise the planet for themselves.
GalahadFairlight
If it was to eradicate us they could have done that millions of years back, why now, so that doesn't add up.
You want to grow the substance (people) that grows your food source before using it. If they waited too much longer, they'd have a harder time because we'd have the technology to fight them back.
The reason which was apparently provided by Wells was that Mars was dying by lack of natural resources and that Martians needed a new home and food source.
They were waiting until the population grew large enough to sustain terraforming efforts. As they used our bodily fluids seemingly as a primary material for their terraforming.
It's an assumption that they could have eradicated us millions of years ago (which by the way would be long before we even existed). Maybe they didn't have the ability to transport themselves, only the machines. Maybe the original aliens all died. Lots of other options why they couldn't have done it.
They probably needed to wait for us to produce enough humans to use as fertilizer. Doesn't make sense to try to use several million bodies as fertilizer back then vs now with billions of people.