Plugin Help Survival Plugin Conflict

So I've been running a Spigot server for some time and I decided to create a survival world to add more gameplay options. When I went to test the overall functionality of the server, I've run into an issue where I:

-Can't damage from Mobs
-// from lava
-// from fall damage
-Mining stone just breaks into stone not cobblestone
-Mining Ore blocks (such as diamond and lapiz) yield the actual ore block (not the ore)

All of this occurs while I'm in survival mode and I have gone through all the configs and such and I can't seem to figure out what is wrong. Perhaps someone can help me.

Here is a list of the plugins that I use:

EssentialsEx
PermissionsEx
WorldEdit
WorldGuard
NoCheatPlus
Chairs
EssentialsChat
EssentialsSpawn
Citizens
EasyWarp
ClearLag
Hats
HideAndCustomePlugins
HolographicDisplays
iDisguise
Multiverse-Core (and portals)
Orebfuscator
PermissionFinder
PlotSquared
ProtocolLib
SetSpawn 2.2.1
ShowCaseStandalone
SignInColors
SilkSpawners
UberEnchant
UltimateHeadFinder
Vault

 

Yes it does