Factual error: When they're near the ferry, the fiery train zooms by. Passenger trains along the Hudson River run along the east bank of the Hudson, not the west bank, where the ferry was departing. (00:56:55)
Factual error: The minivan that Ray drives is shown several times with its rear-most side window rolled all the way down. No such ability exists on any year/model of Chrysler-built minivan. They are either fixed (non-opening) or hinged at their forward edge to open like a 'flap' at the rear edge. The glass isn't broken, as it appears/reappears depending on the scene, and no such customization is possible as such a large window has no place to go down to due to the wheel well location directly below. The windows were obviously removed so the camera could move through the glass without having to use digital effects to go through the window, but in doing so, they created an obvious mistake.
Factual error: When Robbie runs up the hill to watch the army attacking the tripods, Rachel is left standing by a tree and a squadron of AH-1 gunships flies overhead to attack the aliens. However, these helicopters don't have any landing struts (certainly the one nearest the camera doesn't), but all models of the AH-1 had fixed struts.
Factual error: As the Hudson-Athens ferry capsizes, Tom Cruise and his two children are almost crushed as a car slides off the ferry and quickly sinks, going straight to the bottom. We see that this sedan-style car has people in it, and that the windows are closed, so the passenger compartment has not yet flooded. It is still full of air. A sedan full of air would not quickly sink. It would briefly float on the surface, then slowly submerge as the passenger compartment floods.
Factual error: The New York Central Railroad's West Shore Line train tracks depicted in the scene with the burning train in Athens NY is not accurate. Tom Cruise and the children walk right onto the ferry terminal after crossing the train tracks, but in reality the tracks are over two miles to the west of the Hudson River shoreline. (00:57:20)
Factual error: As Tom Cruise and the children walk on route 385 towards Athens NY they pass a sign saying that the town is 1 1/2 miles away just before they cross a bridge. In reality there's no bridge to cross 1 1/2 miles from Athens NY on route 385. (00:56:20)
Factual error: The burning train scene as Tom Cruise leads the children towards the Athens NY ferry is fantastic. The only problem is route 385 does lead them to the center of town but it doesn't intersect a rail line. (00:57:00)
Factual error: The burning train scene in Athens NY is a classic, but not accurate. New York Central Railroad's West Shore Line tracks have been abandoned for years and are not usable. (00:57:15)
Factual error: When Ray comes out from the basement to survey the damage, he sees a crashed plane. As he walks past the fuselage, there is a square window on the cockpit. Planes don't have square windows because to corners were proven stress points from the explosions of two De Havilland Comets in the early 1950's. After the investigations, all plane windows were deemed to be rounded to prevent another such incident.
Factual error: The cars on the ferry would be secured by chains and should not have moved so easily across the deck. Admittedly they would break free at some point depending on the tilt. They had time to secure them, as they were already there before they arrived.
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.