We'll go through the first steps to ensure everything has been setup properly.

1. If you're using Flatfile be sure you're sorting your ranks from Highest to Lowest in the groups.yml.
2. If you're using MySQL be sure to use the command /ne group order Owner Admin Default Ordering Group Priority
3. You will set up your permissions using the permission node you set forth in the command /group [group] perm <value> to the rank associated with it by giving it a true value. You can safely use /nte reload for refreshing/testing ranks.
4. If your ranks are still receiving a different rank then specified. Make sure steps 1 and 2 have been completed.
5. If everything has been properly done and you are still getting the issue. You may need to add the false flag to the last permission node.

In this example, we are going to use nte.guest, nte.citizen.

# Group GUEST
permissions group GUEST create
permissions group GUEST set nte.guest true
permissions group GUEST metadata set prefix "&7&lGUEST &r"
permissions group GUEST setweight 0

# Group CITIZEN
permissions group CITIZEN create
permissions group CITIZEN set nte.citizen true
permissions group CITIZEN set nte.guest false
permissions group CITIZEN metadata set prefix "&3&lCITIZEN &r"
permissions group CITIZEN setweight 0
permissions group CITIZEN setparents GUEST

In this example, the Guest is the first rank, and then Citizen Inherits the Guest Rank and therefore we enable the nte.citizen on the Citizen Rank and disable the Guest Rank use nte.guest false on the permission node.

Are you getting an issue setting up * permissions on your rank?

# Group ADMIN
permissions group ADMIN create
permissions group ADMIN set nte.admin true
permissions group ADMIN set nte.srmod false
permissions group ADMIN metadata set prefix "&2&lADMIN &r"
permissions group ADMIN setweight 0
permissions group ADMIN setparents SR_MOD

# Group OWNER
permissions group OWNER create
permissions group OWNER set nte.admin false
permissions group OWNER set nte.owner true
permissions group OWNER set '*' true
permissions group OWNER metadata set prefix "&4&lOWNER &r"
permissions group OWNER setweight 0
permissions group OWNER setparents ADMIN
permissions group OWNER add 3716427e76ac4df4a50a706618a70f0c/Cory

In this example, I have wildcard permissions, however, since all my ranks have setparents which is the inheritance flag the nte.<rank> false has already been defined and I don't need to define it again.

Note: The permission nodes are based on zPermissions, however, most plugins should follow a similar format.