Command blocks are teleporting people in other dimensions.
If there is a command block in one world that has the command "tp @p[r=5] 128 64 0" it doesn't care what the dimension the nearest player is in. So if a player in another dimension happens to be the one closest to the xyz coordinates, that player would get teleported to the 128,64,0 coordinates in THEIR dimension.

I think command blocks should only be able to teleport players in the dimension the it's placed in, OR there should be another dimension parameter. For example:
"tp @p[r=5,w=dimension]"

I reported this bug to the Spigot team, but they said that this was a vanilla bug. You can see my other report here:
https://hub.spigotmc.org/jira/browse/SPIGOT-851