So, "Dave" gets an MRI. It's a joke involving the electromagnetic machine and his metal body. Okay, funny, haha... but not only the test would accuse something wrong(his whole body is metallic!), the ship itself would probably be fried by the electromagnetic field. Yet nothing wrong happens and everyone acts as if it all went normally... how?
Who said the body was made of metal? It could be emitting false readings for the MRI to pick up.
"Who said the body was made of metal?", you ask? Well, the fact that Dave was involuntarily pulled toward the MRI machine almost in a cartoon-like fashion while the magnets were warming up, and got stuck to the side of it, should be a fairly big implication to that effect.
As for the ship not being damaged by the MRI, keep in mind that the ship was stated to have defensive capabilities; presumably it has a degree of protection against magnetic anomalies such as the MRI.
Okay, apparently no one else thought of this, and maybe I missed an explanation in the movie, but... why do they need to drain the ocean to get salt? Aren't there massive salt warehouses where they can get their fix without killing the Earth?
The people of Nil may not actually know about those salt warehouses, and that's assuming that they could collect enough salt from those warehouses to save their world.
The probe probably homed in on the largest visible concentration of salt on the planet, which is the ocean, the rest is in deposits or mines around the world, plus the probe seems to specifically drain liquids, it was on the ground next to the ocean and didn't seem to activate by harvesting residual salt in the air, perhaps thats how they get salt in general, by extraction of seawater, maybe the reason they need our ocean is because it is roughly the amount needed for whatever their reasons are, they never are clear on why they need so much salt.
Actually, another question to would be "How big is the planet Nil?" The Nilians (?) are tiny and if it needs that much salt to almost drain Earth, then that has to have a few questions.
