Bukkit

What steps will reproduce the problem?
-- I am unsure if I can completely reproduce the problem if I start over and do this but:
1. Download Assassins, Assassination, and Assassin Plugins
2. Set up Permissions Ex (Assassins and Assassin share the same base node [assassin])
3. Run the game?

What is the expected output? What do you see instead?
The expected output is that all plugins work. They did before I set up any permissions.

What version of the product are you using?
Latest since 9/21/2013

Do you have an error log of what happened?
I will quote something from the console logs.

-------------------------[BEGIN QUOTE]-----------------------------
2013-09-21 23:33:37 [WARNING] Plugin Assassins v1.2.2 tried to register permission 'assassin.*' but it's already registered
java.lang.IllegalArgumentException: The permission assassin.* is already defined!
    at org.bukkit.plugin.SimplePluginManager.addPermission(SimplePluginManager.java:572)
    at org.bukkit.craftbukkit.v1_6_R2.CraftServer.loadPlugin(CraftServer.java:288)
    at org.bukkit.craftbukkit.v1_6_R2.CraftServer.enablePlugins(CraftServer.java:264)
    at org.bukkit.craftbukkit.v1_6_R2.CraftServer.reload(CraftServer.java:609)
    at org.bukkit.Bukkit.reload(Bukkit.java:275)
    at org.bukkit.command.defaults.ReloadCommand.execute(ReloadCommand.java:23)
    at org.bukkit.command.SimpleCommandMap.dispatch(SimpleCommandMap.java:191)
    at org.bukkit.craftbukkit.v1_6_R2.CraftServer.dispatchCommand(CraftServer.java:523)
    at org.bukkit.craftbukkit.v1_6_R2.CraftServer.dispatchServerCommand(CraftServer.java:512)
    at net.minecraft.server.v1_6_R2.DedicatedServer.ar(DedicatedServer.java:262)
    at net.minecraft.server.v1_6_R2.DedicatedServer.t(DedicatedServer.java:227)
    at net.minecraft.server.v1_6_R2.MinecraftServer.s(MinecraftServer.java:486)
    at net.minecraft.server.v1_6_R2.MinecraftServer.run(MinecraftServer.java:419)
    at net.minecraft.server.v1_6_R2.ThreadServerApplication.run(SourceFile:582)
-------------------------------[END QUOTE]---------------------------------

Please provide any additional information below.
Using Craft Bukkit 1.6.2 R0.1 and using the following plugins as well.

IGNORE THE * AND THE ~, I was using those to legend something.

Currently Own:
Allow Lockpicking
*Assassin
*Assassins v1.2.2
*BOSEconomy v0.7.8.1
Builder 8.0.1 (Secondary Plugin to Citizens)
*ChestShop
~*Citizens
*Clear Lag
*ColoredSigns
~*Command Kit
~*Command Signs
~*CoreProtect v2.0.8
~*DisguiseCraft
~*Enchant Shops v0.1.4
Enjin Minecraft Plugin
~*Epic Quest
~*Essentials
~*Essentials Chat
~*Essentials Spawn
~*Factions
~*Levels Plus
~LWC
~MCMMO
MCore
*More Potions
*Permissions Ex
Protocol Lib v2.7.0 (Supports DisguiseCraft)
*Random Coords
*Scheduled Announcer
*Survival Games
*Tag API (Supports Assassins Plugin)
Vault
Vote Points
*Votifier
*World Edit
*World Guard

Temporarily Disabled:
*Assassination v1.5.0

Wait, are the nodes assassins.xyz? I just looked at the resources file and noticed that the nodes there say assassins.command.whatever.