I have set groups and prefixes, i also have another plugin for the tab list. I am the owner and can't for the life of me get rid of that stupid tag above my head. Does anyone know anything about this?

Set weight to your ranks. Probably you're getting the perm refer to the [O] prefix.

In case you're using NTE, you should set the jerarquical order by setting the highest rank fist in the list (owner, admin, mod ...)

Unfortunately PermissionsEx is currently unmaintained and no further updates are planned. Because of this, all pull requests are being closed. If you are looking for an actively maintained permissions plugin, take a look at LuckPerms. It is compatible with major server platforms and can import data from PEX.