Great point; although when you look at the Serb paramilitaries, its hard to see any daylight between them and evil. However, you are right on the mark when it comes to the Yugo army.
When fighting the KLA, their outmoded doctrine & poorly trained small unit leaders prevented them from executing the precise fire and maneuver necessary to close with and destroy guerilla forces. Instead, they stood off and used high volumes of fire--usually of little effect against the KLA who slipped away, but likely to cause significant damage to civilians and their homes and livestock and so on. And of course that had the effect of nudging the affected locals further along the spectrum from staying out of the way to sympathizers to supporters to fighters.
I observed many of the same problems, but even more pronounced, at first hand when the Macedonian military was fighting the ethnic Albanian extremists in FYROM in 2001.
An unfortunate side effect of sending an unprepared military to fight a guerilla opponent is that frustration rises rapidly with realization of the ineffectiveness of your tactics; especially if you are also taking casualties. And that frustration provides a fertile breeding ground for atrocities--especially when combined with a lack of professional junior leaders who can enforce discipline. Think My Lai.
Interestingly, Serb tactics the year before last in the Presevo region seemed much improved--constant day & night operations, dispersed small unit patrolling & ambushes. So they're studying lessons learned and getting better. Hopefully they'll next use that stuff for real working with us in the Mid-East!