Globo.com has an article today that explains why the village had issues in some apartments. Apparently, some unsatisfied workers caused the problems in protest because of late payments. Some of the problems these workers caused: put rocks in the toilets, steals some lightbulbs, and constantly making some apartments "dirty" after other workers have cleaned them. Some of these factors couldn't been foreseen (I believe Rio has the first village build with private resources), but the organizing committee admits it should check the buildings as many times as possible before letting anyone set foot there.
As of today, 28 of the 31 buildings are cleared to receive athletes (including the australian one), and the 3 left will be cleared til the end of the day.