So I just installed Vanish No Packet, restarted server, was trying out the commands and after going through pretty much all of them, at least half of them do not work, giving me various errors such as "You can't toggle that!" and "Access Denied". I am fully opped on my server, so I don't understand why it is not working. I am using the correct version, 3.18, and am running the following plugins:
TelePads, Spectate, SWatchdog, WorldEdit, iConomy, PermissionsBukkit, AntiXRay, MCWorld, Vault, WorldGuard, TreeAssist, Essentials, Citizens, EssentialsProtect, EssentialsSpawn, OnTime, EssentialsChat, DtlCitizensTrader, Factions, BattleArena, ArenaSpleef and AntiCheat, however I don't see how any of those would affect this plugin.

Thanks

Read the documentation. OP does not give you very much with VNP :)