I just returned from a month diving Bunaken, Lembeh, Bangka and other sites around North Sulawesi. The plastic you encountered during your dives at Bunaken comes mainly from Manado City and got nothing to do with construction work. Plastic and other trash is ending up in sea because there basically isn't a proper trash pick-up service and locals either dump their trash directly in sea or throw it on the side of the road where a rain-squall will flush it all into the ocean.
In Lembeh Straits trash encountered under water comes from the cargo, tanker and fishing boats and locals that have have their house close to the shoreline. Lembeh Straits trash is worth exploring under water because it's often becoming a habitat for unusual critters. Also, it can be quite amazing what one finds while diving; playing cards, CD's, all sorts of clothing, diapers, sanitary napkins, mugs, small nomination bank notes, dead rats (!), toys, oil filters, engine parts, tyres and heaps of bottles.
There isn't an easy and quick solution for the trash problem around Bunaken (mainly on surface and in mid-water) or for Lembeh Straits but then again; we're doing a great job polluting our oceans all over the world.
Don't let yourself be put down and scared away because of the trash; the diving is absolutely fantastic and the local economy can use your tourist dollars very much.