I have set up the premission system correctly and i can put people in their groups, but for some reason the rank dosent show up before the username.
I need:
[Moderator]JimmyTimmy
I get:
JimmyTimmy

JimmyTimmy has all the commands of the moderator group but not the rank

This isn't Vault issue. Check with your permission system to see if they handle displaying group prefixes etc.