The conflict was between the rebellion organization GAM and the Government represented by the military (TNI). As in many conflicts around the World, the local population becomes a victim of the conflict, and so is the case in Aceh. Both sides were harassing the local population, which resulted in killing of many innocent lives.
The Indonesian government supported and funded non organic troops in Aceh as well, and they were fighting GAM alongside TNI troops. Both sides had also a problem with funding. GAM had few rich supporters, and to compensate for this, extortion became a part of their daily life. The TNI was in a similar situation because only one third of the funds came from the central government in Jakarta, the bulk part of the costs had to be found other places.