They will go indoors, even if there's a housing shortage, and the warning messages aren't always shown. You may have read some posts that were discussing Village Sim (the predecessor to Virtual Villagers), which works a bit differently.

It sounds like you are at the 15-villager limit. The huts you describe are the large building, the love shack and the laundry hut, in addition to the one that your villagers built. The one they are working on will let your population increase to 30 villagers.