I have a factions server to this is a big issue. Any reason my server doesn't spawn non-passive mobs? Passive mobs: Friendly mobs Plugins that may affect the world: WorldGuard, Essentials, EpicWorldGen. NOTE: I know title says Non Passive but I meant passive mobs.
If setting ur difficulty peaceful doenst work try this: Set ur mutliverse settings to /mv modify set monsters true If that doesnt working try this: Spawn some hostile mobs by spawn egg if that works, then try narrowing down a plugin. if that doesnt work: world reset.
Make sure you don't disable them in the servers config.yml, in MultiverseCore config and in WorldGuard config.
Check in spigot.yml, you have a bunch of option like "entity-activation-range" "mob-spawn-range" "nerf-spawner-mobs". and don't forget, passive mobs only spawn on grass blocks from a mob-spawner
Worldguard can stop mobs from spawning, although it would be all mobs and not just passive. If you had the mob-spawning deny on for worldguard globally you would have no mobs. So it's probably being limited by the settings in your bukkit.yml and spigot.yml posting them would help.