Cosmonaut Anatoly Solovyev flew with Space Pens starting in the '80s and states "pencil lead breaks..is not good in space capsule; very dangerous to have metal lead particles in zero gravity".
Strict documentation requirements accompany anything as complex as a large-scale aerospace demonstration, let alone a manned spaceflight.
Personnel may don protective gear, but both ground and flight crews are more comfortable and more productive "in shirtsleeves". Fisher of Fisher Pen Company recounts that pencils were 'too dangerous to use in space'.
Even before the Apollo 1 fire, the CM crew cabin was reviewed for hazardous materials such as paper, velcro, and even low-temperature plastics. When combined with high oxygen content, the Apollo 1 cabin burned within seconds, killing all three crew members.
The laptops used (as of 2012, IBM/Lenovo Think Pads) need customization for space use, such as radiation-, heat- and fire-resistance.
As with submarines before them, space capsules are closed environments, subject to strict contamination requirements. Any shedding, including wood, graphite, and ink vapors and droplets, may become a risk.
In any case, a pen which was insensitive to pressure and temperature would eliminate the issue (including accidental depressurizations), provide a margin, and allow the ability to record during extravehicular activities.
While graphite is claimed to be a hazardous material in space because it burns and conducts electricity, two facts mitigate the risks: 1) the graphite in pencils is mixed with clay during fabrication of the "lead" to help hold its shape, and would only burn at greater than 1,000 °C (1,832 °F); 2) the quantity of graphite particles actually produced during occasional writing would be too small to constitute an electrical hazard.
Low pressures also exacerbate contamination issues, as substances acceptable at standard conditions may begin outgassing at lower pressures or higher temperatures.
While the Soyuz spacecraft had a 14.7 psi (101 k Pa) design pressure, and could use its orbital module as an airlock, the orbital module would be deleted for planned lunar missions.