Ok, So I added my Server to Spiggot 1.12 and Downloaded PermissionsEX to it, but for some reason in-game, when you type in chat, It pops up with 2 groups in your name, and I dont know why.

11.06 16:23:13 [Server] INFO [Owner] *[Owner]*Mawldir: Test

Can someone please tell me how to fix this?

This is a matter of an improperly configured chat management plugin.

Essentials and EssentialsX, for example, both use {group} {displayname} as part of their setup, and the {displayname}variable is a combination of the prefix+username+suffix, combined. So when you define a prefix in PEX, you typically get the result you're seeing. To fix this, look inside your Essentials\config.yml file, down around line 250 or so, and remove the{group}` variable. (See this example for more details.)

Close enough to a week with no response. Case closed, I guess.