Most of the issues with these runway overruns in this part of the world are human factors related. Jogja has had two major runway excursions prior to this; one with a Sriwijaya 737-300 in December 2011 and the Garuda GA 200 accident in March 2007 resulting in fatalities.
The GA200 final report is sobering reading. Warnings And alerts going off in the cockpit, a vocal FO but not willing to take over.
http://avherald.com/h?article=3f0bff36/0041&opt=0
http://avherald.com/h?article=447f70f9