Ananda, at the time of the East Timor crisis, were there many troops of East Timorese descent serving in the TN-AD? With regards to firefights, as Kirkzzy pointed out there's no point in speculating on what we don't know and what has yet to be officially confirmed but there is a strong possibility that certain incidents may have been done by rogue troops acting without authorisation.
No, that one of the mistakes that Mindef learn after East Timor and Aceh Insurgences. The face of the Army was to Javanise, and not enough local content. Thus the cohessions between local people and the Army at that area in that time was very low.
Currently the number of local recruit in Papua or soldiers that come from near islands (like mollacas/maluku) are more present in the Army contingent in Papua/Irian. This again to improved the face of the Army in the local people perspective. This especially so in trouble area like Papua now, whille in most part of Indonesia this not really matter due to stronger sense of Nationalistic in local People of otherpart of Indonesia.
In other word, People of East Timor did not feel they belong to Indonesia for most part, and the Indonesian sociaty it self for most part did not try enough to embraced east timor people (even the west timor still suspicious in many part to east timorese). Whille people in Aceh and Papua feel they can still belong to Indonesia, but feel the Government (at that time) left them behind.
That's why, after Acehnese got their own local government with their liking, they mostly calmed down. Whille many papuan especially on the west side of Indonesian Irian/Papua, mostly more acceptive right now when many recruits of local Government now and Police plus Army comming from their rank.
Like i said before, based on the data and media, no Indonesian regulars that lurking back to East Timor after the pull-out. This is the time after Soeharto, and the Media was on extensive mood for their new found freedom. That kind ofthing if happnes can't be contain from the Media.
But some of the units (especially Kopassus) did left behind some of their equipment to their proxy militia. That's what the Aussies particularly has to handle, after TNI pull out.