When changing clear weather to rain or thunder, looking up will generate this pattern instead of showing that rain is actually falling on the player. When you move around while looking up during rain, this "empty space" in the rain will follow you but it is stuck to the block grid.
When looking down, you can see lines of empty space appear in the directions of the player to
N, NW, NE, E, SE, SW. Look at the screen shot to know what I mean. This bug is more noticeable in the weather mode "thunder."