I saw an argument a while back that, given the amount of kryptonite on Earth, either the planet Krypton was larger than our solar system or the kryptonite was deliberately sent with Clark's ship for some reason. The idea makes sense to me.
What if kryptonite were part of the ship as a power source and some remained inside it somewhere for Trask to find? From the construction I think an alien would be able to figure out that uranium is necessary for a nuclear submarine to operate, but the shielding and safeguards show we wouldn't want to have contact with it. The shielding would be a clue for Trask that the stuff would be harmful to a Kryptonian.
I like the idea that kryptonite was part of the ship's life support system. Shielded and in controlled doses and with no other energy source, the kryptonite kept Clark alive. Here on Earth and with an abundance of energy stored in his body the kryptonite is dangerous to Clark.
