Singapore occasionally disembarks flights from places with "substandard" security procedures into additional screening. It's been that way for years. As pointed out, since connecting to any other flight requires screening, it's always seemed a bit unnecessary to me, but that's the way they do it.
Flights from Indonesia and the Philippines are the usual suspects to trigger this, as the OP found out. I believe there's a thread either in the Singapore or the SQ forum on this, though it's a few years old by now.