Why does the Martian's weapon leave clothing intact? Its an highly-focused enhanced radiation weapon similar to a Neutron Bomb, which is designed to wipe out enemies soldiers but leave their infrastructure relatively intact. This is why it dessicates humans into ash but less of an effect on clothing (and armour). Similarly, it also demonstrates similarlities to a neutron bomb's having some concussive force, in the way that it impacts objects. It isn't a "heat ray" at all, as throughout the films, we never see it ignite objects, the only fires seen are clearly caused by explosions from other sources.
When the aliens go through Ogilvy's basement, they all look at a picture of what's presumed to be Ogilvy's deceased daughter. Notice that they all look at it the wrong way (as in, never viewing it upright). Common from something that's never seen a photograph before.
The aliens somehow get gigantic war-vehicles to come out of the ground. See the Headscratcher page for more in-depth discussion.
The plants that the Martians are growing are a vein like substance If you wonder why they chose this design was because one of the writers Percival Lowell who used an observatory to research mars and it's "Canal S" However these canals were actually the veins inside his eyeballs.