This is a fairly severe issue. I run a vanilla server with plenty of command blocks, and created a dummy entity to mark the server's spawn point. The point of this was to run execute commands against the spawn entity to set up spawn protection so players can't attack one another while at spawn. In the most recent updates, this broke. Even though the spawn entity is ONLY in the overworld, the commands it is running (which is all based on relative radius and whatnot) affect every dimension, as opposed to only the overworld, which breaks so many things I can't even begin to list it... Please fix this.