Rain coming through blocks, and randomly dying after trying to change the bugged out rain.

So I was making a 1x1 pillar of raw iron Ore blocks and after I got done placing the last Ore block. I tried to enter in the command /weather clear. As I got done typing it, I sent it through took a couple seconds it made the command but then it killed me. Saying that I died from falling from a high place. And then after I died and respawned the rain was coming through my house that was still bugged. I know how to fix the bugged rain but it was just coming through my ceiling.