The confusion is that Malaya is the mainland part of the country known as Malaysia, which includes various overseas provinces, where this happened.

All colonial wars include atrocities, it seems pretty safe to say. All wars include atrocities for that matter. "Atrocity" meaning an atrocious thing that is against the rules, and in theory would count as war crimes, unlike other things that may be equally or even more atrocious, that aren't against the rules, and don't count as war crimes.

Taking body parts as souvenirs would count as being a war crime I believe, at least in theory. It would also be seen as a military offence, which potentially could be treated seriously. Sometimes it has been.