Water injested into engine

I had my engine replaced in a 525i bmw after it injested water. One month later my wife was drive in a rain storm and the car begin to shake, it shut off and would not start back up. I had it towed to the shop and they are saying it injested water again through the intake manifold. A 12k rebuilded engine and in the very first rain we have injest water??This makes no sense to me. Have you ever heard of this happening. If so, what is causing water to enter into the manifold?