The graphite/carbon in a pencil reacts at high temperatures causing a corrosive failure point. If you were to mark the hot section of a turbine (inside or outside), it would lead to the same type of damage as if you cut a hole in the can with a torch.

I remember a new crewchief of mine, who thought he was doing the right thing, circled every little ping on the hot end of my AH-1F Cobra engine. Our Maintenance Officer saw this and came uncorked! He immediately "Red-X'd" the aircraft and ordered an entire hot end change. From what I understand, even if you attempt to clean the pencil off, the trace amounts left behind in the porous steel is enough to cause failure.

Craig