For the little that I have read about the subject there were not any skirmishes between those Japanese obeying Allied orders and those joining the Indonesian independence movement. The Japanese in autumn 1945 had absolutely no interest to take any action against Indonesian independence movement in behalf of the Allied (Dutch) but were in many cases sympathetic and cooperative to Indonesian independence movement:
https://www.youtube.com/watch?v=z9tYurVJKG4
There has been some academic studies of the theme:
http://journals.cambridge.org/action...ne&aid=7445000
This is one of those points when things are more complicated than the simple perfection of WW2 combatants as the "evil Axis" and the "good Allied". In Indonesia many Japanese soldiers ended up to be the "good guys" - freedom fighters against the "bad guys" = the Western Allied (British/Dutch) who tried to restore the colonial yoke of Europeans. The "bad guy/good guy" depends from the point of view and is complicated issue here. Interestingly some Japanese soldiers ended up to be at the winning side after all when Indonesia gained its independence.
More of the theme:
http://www.thejakartapost.com/news/2...a-dies-95.html
http://www.japantimes.co.jp/news/201.../#.VfAvaPysV8E
http://www.amazon.com/Japanese-Memoi.../dp/6028397199
About the Japanese who fought for the Indonesian independence their motives may have been mixed: it seems some indeed genuinely supported the Indonesian cause and perhaps some were mercenaries - I wonder if the latter category included the Japanese pilots of the nascent Indonesian Air Force.
In any case the Japanese played a very important, even fundamental role in building up, training and equipping the Indonesians for the later independence war against the Dutch.