There are a few different methods. The plastic should not be against the floor joists, ever. Some vapor barriers are plastic on the ground, then covered by pea gravel. Some are plastic straight on a pea gravel or sand "bedding." Others are plastic on the ground and up the walls. The idea for all of them is to keep moisture from humidity and/or ground water from getting to the joists and floor decking. If you're getting noticeable water, I'd have the barrier checked. If it is on the floors and up the walls and still intact, you may have a whole other issue.