According to the guide, it looks like it's the scene in jail where Ash gets beat in a fight. Ash has to be bad enough to go to jail, but good enough to surrender in the fight. So it's a karma balance thing rather than getting certain flags set. I don't think there is anything specific anyone could tell him other than keep an eye on Karma throughout the playthrough.which scene is it?
Or just edit the karma like I suggested if it's to much hassle.