This might not be a bug, but I've looked through the Spigot and Bukkit settings several times and there seems to be no way to turns this behavior off so now I'm going to assume it's a bug. To make sure this wasn't just me, I first posted a discussion thread about it, where others confirmed seeing the same behavior. You can find that here:
http://www.spigotmc.org/threads/anyone-noticed-that-command-blocks-work-through-worlds.63231/#post-703081

As the title states, command blocks seems to act through worlds. If I enter "tp @p 0 100 0" it would take the closest player, not considering if they're actually in the world or not. So if the closest player is in another world, that player will be picked.

My server runs several different matches which are all in different worlds. People are getting randomly teleported sometimes because of this issue and you can probably see why I'd like this fixed.