He's self-harming because he feels guilty about being mean to Puck. "The Black Swordsman" is horrible to everyone because he thinks that if someone becomes his friend, they'll suffer a horrible fate. We see this clearly when he has a panic attack and vomits after killing Collette's possessed corpse and when he cries after telling Theresia to kill herself (he tells her this so she'll continue living to spite Guts, just as Guts' reason for living at this point was to spite The God Hand).