Trying to denote this permission from a second world, but it does nothing if you allow it or deny it.

What do you mean by "denote"?
(I'm not a native speaker)

Make false in permissions to disable it, in certain worlds.

- simpleclans.member.ally:
    world: world_nether
    value: false

I see.
So, members with this permission denied are still able to use the chat?

Yup, thats right!
Basically I have a "punihsment" world, where I don't want them to talk at all, in global chat or ally/crew chat, I think the crew chat permission is the same, so im trying to deny them the use, so when there in a punishment they cant talk!

What permissions plugin do you use?

Luckperms sorry I must have missed this reply!

Apparently, the plugin was not checking if players had this permission.
Let me know if this update fixes it: https://1drv.ms/u/s!Av2G_9O8Vhlhptp11P3noTf8HvE59w

P.S.: Jenkins seems to be off, so I'm sharing from my OneDrive.