I have a border system as well for the Overworld and Nether. Im using x y z dx dy dz so the commands only work on those dimension, but the commands from the nether is affecting my players in the overworld.
I think we found out what happened, this can be close now.
Another player reported to me that his base got laggy, this happens after they made the spawner into a mob grinder, which I think this happened because they failed to kill the mobs and transformed into entity None
I'm not sure how, but it happened on events where entity were crammed like spawners or bred animals like cow. I also notice mobs freezes when I teleport to a player near them and they became invincible, maybe that's one of the reason, I might have teleported to a player with crowded mobs and they freezes, if you hit them once, they can't be hit again, that might be it, for some reason, it leaves an entity even though they are dead or disappeared.
Repeat
Unconditional
Always Active
posx-posz
effect @a[tag=!admin, x=1300, y=0, z=1300, dx=5000, dy=512, dz=-15000] fatal_poison 5 3
Chain
Conditional
Always Active
§c§lBorder[N]
say @p[tag=!admin, x=1300, y=0, z=1300, dx=5000, dy=512, dz=-15000] §cTurn back or the world border will kill you!
not sure if this will help. Like I said, since an x y z dx dy dz are present, it should only work on that dimension.