I've seen spots like that from the metallic particles in the clutch disk rusting while sitting. Then when you run the engine they scuff like that because the rust has penetrated both the flywheel and pressure plate. It doesn't take long - I had that happen in about a month's time.

As for wearing on one side only it could be from uneven spring pressure but it could also be because only that side of the assembly rusted - more moisture in that side of the disk - although why, I can't imagine.