After watching the movie a couple of times I noticed something. Geo stigma is being infected with jenova cells. If that's the case then why is cloud infected/sick if he already has jenova cells in him because of being SOLDIER. Also sephiroth can't get infected with his own gene so how come cloud can if he is a(failed)clone? Is this a loophole in the plot or am I missing something?
Geostigma is Jenova cells that have been diffused in the Lifestream. The cells act like a virus in the bloodstream of the planet. Lifestream energy is in everyone, so if the Lifestream is infected and under attack, than so is everyone else. However, it is not a physical thing that can be fought off via immune system, but the body is still trying to repel the invader it knows is there but can't really find. Thus the blackening of the skin, as the body is actually attacking itself.
Now, keep in mind that Sephiroth has Jenova in his DNA-it is part of his being. Cloud, on the other hand, is thouroughly human. Yes, he was shot full of Jenova cells, but the normal human cells were affected and changed in the presence of the Jenova cells--different but still human. This would be known as a mutation. So Sephiroth is a human/alien half breed, but Cloud, while different, is a human. And so Cloud can be infected by Geostigma.