In a server that I've been working on, we put command blocks at spawn to protect it and give players effects, change gamemodes, etc, but when I go to the coordinates of overworld spawn in the nether (which happens to be near where the nether portal spawned), the command blocks affect me as if I were in the overworld. Basically meaning that they set me to adventure mode, and give me resistance, despite no command blocks even being present. This is preventing players from editing part of the nether. I haven't checked the end yet, but if it's happening there, too, then it could end up giving them an unfair advantage in the fight with the dragon due to the resistance effect, or it would prevent them from mining endstone or respawning the dragon.