If multiple jukeboxes are playing the same disc, taking one of the discs out of one of the jukeboxes will make all jukeboxes stop playing the disc.

Related to #16. This issue may be impossible to fix, because Minecraft does not have a way to reference specific sounds. So if you have two jukeboxes next to each other, there's no way for the /stopsound command to target a particular one.

The datapack does have a distance check, so custom music discs playing far apart won't affect each other.